1
|
Andorfer MC, King-Roberts DT, Imrich CN, Brotheridge BG, Drennan CL. Development of an in vitro method for activation of X-succinate synthases for fumarate hydroalkylation. iScience 2023; 26:106902. [PMID: 37283811 PMCID: PMC10239695 DOI: 10.1016/j.isci.2023.106902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 05/08/2023] [Accepted: 05/12/2023] [Indexed: 06/08/2023] Open
Abstract
Anaerobic microbial degradation of hydrocarbons is often initiated through addition of the hydrocarbon to fumarate by enzymes known as X-succinate synthases (XSSs). XSSs use a glycyl radical cofactor, which is installed by an activating enzyme (XSS-AE), to catalyze this carbon-carbon coupling reaction. The activation step, although crucial for catalysis, has not previously been possible in vitro because of insolubility of XSS-AEs. Here, we take a genome mining approach to find an XSS-AE, a 4-isopropylbenzylsuccinate synthase (IBSS)-AE (IbsAE) that can be solubly expressed in Escherichia coli. This soluble XSS-AE can activate both IBSS and the well-studied benzylsuccinate synthase (BSS) in vitro, allowing us to explore XSSs biochemically. To start, we examine the role of BSS subunits and find that the beta subunit accelerates the rate of hydrocarbon addition. Looking forward, the methodology and insight gathered here can be used more broadly to understand and engineer XSSs as synthetically useful biocatalysts.
Collapse
Affiliation(s)
- Mary C. Andorfer
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Devin T. King-Roberts
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Christa N. Imrich
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Balyn G. Brotheridge
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Catherine L. Drennan
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Center for Environmental Health, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Bio-inspired Solar Energy Program, Canadian Institute for Advanced Research (CIFAR), Toronto, ON M5G 1M1, Canada
| |
Collapse
|
2
|
Fu B, Nazemi A, Levin BJ, Yang Z, Kulik HJ, Balskus EP. Mechanistic Studies of a Skatole-Forming Glycyl Radical Enzyme Suggest Reaction Initiation via Hydrogen Atom Transfer. J Am Chem Soc 2022; 144:11110-11119. [PMID: 35704859 PMCID: PMC9248008 DOI: 10.1021/jacs.1c13580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
Gut microbial decarboxylation
of amino acid-derived arylacetates
is a chemically challenging enzymatic transformation which generates
small molecules that impact host physiology. The glycyl radical enzyme
(GRE) indoleacetate decarboxylase from Olsenella uli (Ou IAD) performs the non-oxidative radical decarboxylation
of indole-3-acetate (I3A) to yield skatole, a disease-associated metabolite
produced in the guts of swine and ruminants. Despite the importance
of IAD, our understanding of its mechanism is limited. Here, we characterize
the mechanism of Ou IAD, evaluating previously proposed
hypotheses of: (1) a Kolbe-type decarboxylation reaction involving
an initial 1-e– oxidation of the carboxylate of
I3A or (2) a hydrogen atom abstraction from the α-carbon of
I3A to generate an initial carbon-centered radical. Site-directed
mutagenesis, kinetic isotope effect experiments, analysis of reactions
performed in D2O, and computational modeling are consistent
with a mechanism involving initial hydrogen atom transfer. This finding
expands the types of radical mechanisms employed by GRE decarboxylases
and non-oxidative decarboxylases, more broadly. Elucidating the mechanism
of IAD decarboxylation enhances our understanding of radical enzymes
and may inform downstream efforts to modulate this disease-associated
metabolism.
Collapse
Affiliation(s)
- Beverly Fu
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Azadeh Nazemi
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Benjamin J Levin
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Zhongyue Yang
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Heather J Kulik
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Emily P Balskus
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States.,Howard Hughes Medical Institute, Harvard University, Cambridge, Massachusetts 02138, United States
| |
Collapse
|
3
|
McLean JT, Benny A, Nolan MD, Swinand G, Scanlan EM. Cysteinyl radicals in chemical synthesis and in nature. Chem Soc Rev 2021; 50:10857-10894. [PMID: 34397045 DOI: 10.1039/d1cs00254f] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Nature harnesses the unique properties of cysteinyl radical intermediates for a diverse range of essential biological transformations including DNA biosynthesis and repair, metabolism, and biological photochemistry. In parallel, the synthetic accessibility and redox chemistry of cysteinyl radicals renders them versatile reactive intermediates for use in a vast array of synthetic applications such as lipidation, glycosylation and fluorescent labelling of proteins, peptide macrocyclization and stapling, desulfurisation of peptides and proteins, and development of novel therapeutics. This review provides the reader with an overview of the role of cysteinyl radical intermediates in both chemical synthesis and biological systems, with a critical focus on mechanistic details. Direct insights from biological systems, where applied to chemical synthesis, are highlighted and potential avenues from nature which are yet to be explored synthetically are presented.
Collapse
Affiliation(s)
- Joshua T McLean
- Trinity Biomedical Sciences Institute, Trinity College Dublin, The University of Dublin, 152-160 Pearse St., Dublin, D02 R590, Ireland.
| | - Alby Benny
- Trinity Biomedical Sciences Institute, Trinity College Dublin, The University of Dublin, 152-160 Pearse St., Dublin, D02 R590, Ireland.
| | - Mark D Nolan
- Trinity Biomedical Sciences Institute, Trinity College Dublin, The University of Dublin, 152-160 Pearse St., Dublin, D02 R590, Ireland.
| | - Glenna Swinand
- Trinity Biomedical Sciences Institute, Trinity College Dublin, The University of Dublin, 152-160 Pearse St., Dublin, D02 R590, Ireland.
| | - Eoin M Scanlan
- Trinity Biomedical Sciences Institute, Trinity College Dublin, The University of Dublin, 152-160 Pearse St., Dublin, D02 R590, Ireland.
| |
Collapse
|
4
|
Salii I, Szaleniec M, Zein AA, Seyhan D, Sekuła A, Schühle K, Kaplieva-Dudek I, Linne U, Meckenstock RU, Heider J. Determinants for Substrate Recognition in the Glycyl Radical Enzyme Benzylsuccinate Synthase Revealed by Targeted Mutagenesis. ACS Catal 2021. [DOI: 10.1021/acscatal.0c04954] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Iryna Salii
- Department of Biology, Laboratory for Microbial Biochemistry, Philipps University Marburg, 35043 Marburg, Germany
- Synmikro-Center for Synthetic Microbiology, Philipps University Marburg, 35043 Marburg, Germany
| | - Maciej Szaleniec
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Science, 30-239 Kraków, Poland
| | - Ammar Alhaj Zein
- Department of Biology, Laboratory for Microbial Biochemistry, Philipps University Marburg, 35043 Marburg, Germany
- Synmikro-Center for Synthetic Microbiology, Philipps University Marburg, 35043 Marburg, Germany
| | - Deniz Seyhan
- Department of Biology, Laboratory for Microbial Biochemistry, Philipps University Marburg, 35043 Marburg, Germany
- Synmikro-Center for Synthetic Microbiology, Philipps University Marburg, 35043 Marburg, Germany
| | - Anna Sekuła
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Science, 30-239 Kraków, Poland
| | - Karola Schühle
- Department of Biology, Laboratory for Microbial Biochemistry, Philipps University Marburg, 35043 Marburg, Germany
- Synmikro-Center for Synthetic Microbiology, Philipps University Marburg, 35043 Marburg, Germany
| | | | - Uwe Linne
- Synmikro-Center for Synthetic Microbiology, Philipps University Marburg, 35043 Marburg, Germany
- Department of Chemistry, Philipps University Marburg, 35043 Marburg, Germany
| | | | - Johann Heider
- Department of Biology, Laboratory for Microbial Biochemistry, Philipps University Marburg, 35043 Marburg, Germany
- Synmikro-Center for Synthetic Microbiology, Philipps University Marburg, 35043 Marburg, Germany
| |
Collapse
|
5
|
Backman LRF, Funk MA, Dawson CD, Drennan CL. New tricks for the glycyl radical enzyme family. Crit Rev Biochem Mol Biol 2017; 52:674-695. [PMID: 28901199 DOI: 10.1080/10409238.2017.1373741] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Glycyl radical enzymes (GREs) are important biological catalysts in both strict and facultative anaerobes, playing key roles both in the human microbiota and in the environment. GREs contain a backbone glycyl radical that is post-translationally installed, enabling radical-based mechanisms. GREs function in several metabolic pathways including mixed acid fermentation, ribonucleotide reduction and the anaerobic breakdown of the nutrient choline and the pollutant toluene. By generating a substrate-based radical species within the active site, GREs enable C-C, C-O and C-N bond breaking and formation steps that are otherwise challenging for nonradical enzymes. Identification of previously unknown family members from genomic data and the determination of structures of well-characterized GREs have expanded the scope of GRE-catalyzed reactions as well as defined key features that enable radical catalysis. Here, we review the structures and mechanisms of characterized GREs, classifying members into five categories. We consider the open questions about each of the five GRE classes and evaluate the tools available to interrogate uncharacterized GREs.
Collapse
Affiliation(s)
- Lindsey R F Backman
- a Department of Chemistry , Massachusetts Institute of Technology , Cambridge , MA , USA
| | - Michael A Funk
- a Department of Chemistry , Massachusetts Institute of Technology , Cambridge , MA , USA.,b Department of Chemistry , University of Illinois at Urbana-Champaign , Urbana , IL , USA
| | - Christopher D Dawson
- c Department of Biology , Massachusetts Institute of Technology , Cambridge , MA , USA
| | - Catherine L Drennan
- a Department of Chemistry , Massachusetts Institute of Technology , Cambridge , MA , USA.,c Department of Biology , Massachusetts Institute of Technology , Cambridge , MA , USA.,d Howard Hughes Medical Institute , Massachusetts Institute of Technology , Cambridge , MA , USA
| |
Collapse
|
6
|
Seyhan D, Friedrich P, Szaleniec M, Hilberg M, Buckel W, Golding BT, Heider J. Stereochemischer Verlauf der enzymatischen Synthese von Benzylsuccinat mit chiral markiertem Toluol. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201605197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Deniz Seyhan
- Laboratorium für Mikrobielle Biochemie und Synmikro-Zentrum für synthetische Mikrobiologie; Philipps Universität Marburg; 35043 Marburg an der Lahn Deutschland
| | - Peter Friedrich
- School of Chemistry, Bedson Building; Newcastle University; Newcastle upon Tyne NE1 7RU Großbritannien
| | - Maciej Szaleniec
- Jerzy Haber Institute of Catalysis and Surface Chemistry; Polish Academy of Science; 30-239 Krakau Polen
| | - Markus Hilberg
- Laboratorium für Mikrobielle Biochemie und Synmikro-Zentrum für synthetische Mikrobiologie; Philipps Universität Marburg; 35043 Marburg an der Lahn Deutschland
| | - Wolfgang Buckel
- Max-Planck-Institut für terrestrische Mikrobiologie; 35043 Marburg an der Lahn Deutschland
| | - Bernard T. Golding
- School of Chemistry, Bedson Building; Newcastle University; Newcastle upon Tyne NE1 7RU Großbritannien
| | - Johann Heider
- Laboratorium für Mikrobielle Biochemie und Synmikro-Zentrum für synthetische Mikrobiologie; Philipps Universität Marburg; 35043 Marburg an der Lahn Deutschland
| |
Collapse
|
7
|
Seyhan D, Friedrich P, Szaleniec M, Hilberg M, Buckel W, Golding BT, Heider J. Elucidating the Stereochemistry of Enzymatic Benzylsuccinate Synthesis with Chirally Labeled Toluene. Angew Chem Int Ed Engl 2016; 55:11664-7. [PMID: 27503670 DOI: 10.1002/anie.201605197] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Revised: 07/01/2016] [Indexed: 11/08/2022]
Abstract
Benzylsuccinate synthase is a glycyl radical enzyme that initiates anaerobic toluene metabolism by adding fumarate to the methyl group of toluene to yield (R)-benzylsuccinate. To investigate whether the reaction occurs with retention or inversion of configuration at the methyl group of toluene, we synthesized both enantiomers of chiral toluene with all three H isotopes in their methyl groups. The chiral toluenes were converted into benzylsuccinates preferentially containing (2) H and (3) H at their benzylic C atoms, owing to a kinetic isotope effect favoring hydrogen abstraction from the methyl groups. The configuration of the products was analyzed by enzymatic CoA-thioester synthesis and stereospecific oxidation using enzymes involved in benzylsuccinate degradation. Assessment of the configurations of the benzylsuccinate isomers based on loss or retention of tritium showed that inversion of configuration at the methyl group occurs when the chiral toluenes react with fumarate.
Collapse
Affiliation(s)
- Deniz Seyhan
- Laboratorium für Mikrobielle Biochemie and Synmikro-Zentrum für synthetische Mikrobiologie, Philipps Universität Marburg, 35043, Marburg an der Lahn, Germany
| | - Peter Friedrich
- School of Chemistry, Bedson Building, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Maciej Szaleniec
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Science, 30-239, Kraków, Poland
| | - Markus Hilberg
- Laboratorium für Mikrobielle Biochemie and Synmikro-Zentrum für synthetische Mikrobiologie, Philipps Universität Marburg, 35043, Marburg an der Lahn, Germany
| | - Wolfgang Buckel
- Max-Planck-Institut für terrestrische Mikrobiologie, 35043, Marburg an der Lahn, Germany
| | - Bernard T Golding
- School of Chemistry, Bedson Building, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Johann Heider
- Laboratorium für Mikrobielle Biochemie and Synmikro-Zentrum für synthetische Mikrobiologie, Philipps Universität Marburg, 35043, Marburg an der Lahn, Germany.
| |
Collapse
|
8
|
Heider J, Szaleniec M, Martins BM, Seyhan D, Buckel W, Golding BT. Structure and Function of Benzylsuccinate Synthase and Related Fumarate-Adding Glycyl Radical Enzymes. J Mol Microbiol Biotechnol 2016; 26:29-44. [PMID: 26959246 DOI: 10.1159/000441656] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The pathway of anaerobic toluene degradation is initiated by a remarkable radical-type enantiospecific addition of the chemically inert methyl group to the double bond of a fumarate cosubstrate to yield (R)-benzylsuccinate as the first intermediate, as catalyzed by the glycyl radical enzyme benzylsuccinate synthase. In recent years, it has become clear that benzylsuccinate synthase is the prototype enzyme of a much larger family of fumarate-adding enzymes, which play important roles in the anaerobic metabolism of further aromatic and even aliphatic hydrocarbons. We present an overview on the biochemical properties of benzylsuccinate synthase, as well as its recently solved structure, and present the results of an initial structure-based modeling study on the reaction mechanism. Moreover, we compare the structure of benzylsuccinate synthase with those predicted for different clades of fumarate-adding enzymes, in particular the paralogous enzymes converting p-cresol, 2-methylnaphthalene or n-alkanes.
Collapse
Affiliation(s)
- Johann Heider
- Laboratory of Microbial Biochemistry, LOEWE Center for Synthetic Microbiology, Philipps University Marburg, Marburg, Germany
| | | | | | | | | | | |
Collapse
|
9
|
Lesslie M, Lau JKC, Lawler JT, Siu KWM, Steinmetz V, Maître P, Hopkinson AC, Ryzhov V. Cysteine Radical/Metal Ion Adducts: A Gas-Phase Structural Elucidation and Reactivity Study. Chempluschem 2016; 81:444-452. [DOI: 10.1002/cplu.201500558] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Indexed: 12/22/2022]
Affiliation(s)
- Michael Lesslie
- Department of Chemistry and Biochemistry; Northern Illinois University; DeKalb IL 60115 USA
| | - Justin Kai-Chi Lau
- Department of Chemistry and Centre for Research in Mass Spectrometry; York University; Toronto ON M3J 1P3 Canada
- Department of Chemistry and Biochemistry; University of Windsor; Windsor ON N9B 3P4 Canada
| | - John T. Lawler
- Department of Chemistry and Biochemistry; Northern Illinois University; DeKalb IL 60115 USA
| | - K. W. Michael Siu
- Department of Chemistry and Centre for Research in Mass Spectrometry; York University; Toronto ON M3J 1P3 Canada
- Department of Chemistry and Biochemistry; University of Windsor; Windsor ON N9B 3P4 Canada
| | - Vincent Steinmetz
- Laboratoire de Chimie Physique; Université Paris-Sud; UMR8000 CNRS; 91405 Orsay France
| | - Philippe Maître
- Laboratoire de Chimie Physique; Université Paris-Sud; UMR8000 CNRS; 91405 Orsay France
| | - Alan C. Hopkinson
- Department of Chemistry and Centre for Research in Mass Spectrometry; York University; Toronto ON M3J 1P3 Canada
| | - Victor Ryzhov
- Department of Chemistry and Biochemistry; Northern Illinois University; DeKalb IL 60115 USA
| |
Collapse
|
10
|
Bharadwaj VS, Vyas S, Villano SM, Maupin CM, Dean AM. Unravelling the impact of hydrocarbon structure on the fumarate addition mechanism--a gas-phase ab initio study. Phys Chem Chem Phys 2016; 17:4054-66. [PMID: 25566585 DOI: 10.1039/c4cp04317k] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The fumarate addition reaction mechanism is central to the anaerobic biodegradation pathway of various hydrocarbons, both aromatic (e.g., toluene, ethyl benzene) and aliphatic (e.g., n-hexane, dodecane). Succinate synthase enzymes, which belong to the glycyl radical enzyme family, are the main facilitators of these biochemical reactions. The overall catalytic mechanism that converts hydrocarbons to a succinate molecule involves three steps: (1) initial H-abstraction from the hydrocarbon by the radical enzyme, (2) addition of the resulting hydrocarbon radical to fumarate, and (3) hydrogen abstraction by the addition product to regenerate the radical enzyme. Since the biodegradation of hydrocarbon fuels via the fumarate addition mechanism is linked to bio-corrosion, an improved understanding of this reaction is imperative to our efforts of predicting the susceptibility of proposed alternative fuels to biodegradation. An improved understanding of the fuel biodegradation process also has the potential to benefit bioremediation. In this study, we consider model aromatic (toluene) and aliphatic (butane) compounds to evaluate the impact of hydrocarbon structure on the energetics and kinetics of the fumarate addition mechanism by means of high level ab initio gas-phase calculations. We predict that the rate of toluene degradation is ∼100 times faster than butane at 298 K, and that the first abstraction step is kinetically significant for both hydrocarbons, which is consistent with deuterium isotope effect studies on toluene degradation. The detailed computations also show that the predicted stereo-chemical preference of the succinate products for both toluene and butane are due to the differences in the radical addition rate constants for the various isomers. The computational and kinetic modeling work presented here demonstrates the importance of considering pre-reaction and product complexes in order to accurately treat gas phase systems that involve intra and inter-molecular non-covalent interactions.
Collapse
Affiliation(s)
- Vivek S Bharadwaj
- Chemical and Biological Engineering Department, Colorado School of Mines, 1500 Illinois Street, Golden, CO 80401, USA.
| | | | | | | | | |
Collapse
|
11
|
Jarling R, Kühner S, Basílio Janke E, Gruner A, Drozdowska M, Golding BT, Rabus R, Wilkes H. Versatile transformations of hydrocarbons in anaerobic bacteria: substrate ranges and regio- and stereo-chemistry of activation reactions. Front Microbiol 2015; 6:880. [PMID: 26441848 PMCID: PMC4561516 DOI: 10.3389/fmicb.2015.00880] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Accepted: 08/10/2015] [Indexed: 12/31/2022] Open
Abstract
Anaerobic metabolism of hydrocarbons proceeds either via addition to fumarate or by hydroxylation in various microorganisms, e.g., sulfate-reducing or denitrifying bacteria, which are specialized in utilizing n-alkanes or alkylbenzenes as growth substrates. General pathways for carbon assimilation and energy gain have been elucidated for a limited number of possible substrates. In this work the metabolic activity of 11 bacterial strains during anaerobic growth with crude oil was investigated and compared with the metabolite patterns appearing during anaerobic growth with more than 40 different hydrocarbons supplied as binary mixtures. We show that the range of co-metabolically formed alkyl- and arylalkyl-succinates is much broader in n-alkane than in alkylbenzene utilizers. The structures and stereochemistry of these products are resolved. Furthermore, we demonstrate that anaerobic hydroxylation of alkylbenzenes does not only occur in denitrifiers but also in sulfate reducers. We propose that these processes play a role in detoxification under conditions of solvent stress. The thermophilic sulfate-reducing strain TD3 is shown to produce n-alkylsuccinates, which are suggested not to derive from terminal activation of n-alkanes, but rather to represent intermediates of a metabolic pathway short-cutting fumarate regeneration by reverse action of succinate synthase. The outcomes of this study provide a basis for geochemically tracing such processes in natural habitats and contribute to an improved understanding of microbial activity in hydrocarbon-rich anoxic environments.
Collapse
Affiliation(s)
- René Jarling
- Organic Geochemistry, Chemistry of the Earth, Helmholtz Centre Potsdam GFZ German Research Centre for Geosciences Potsdam, Germany
| | - Simon Kühner
- Department of Microbiology, Max Planck Institute for Marine Microbiology Bremen, Germany
| | - Eline Basílio Janke
- Organic Geochemistry, Chemistry of the Earth, Helmholtz Centre Potsdam GFZ German Research Centre for Geosciences Potsdam, Germany
| | - Andrea Gruner
- Organic Geochemistry, Chemistry of the Earth, Helmholtz Centre Potsdam GFZ German Research Centre for Geosciences Potsdam, Germany
| | - Marta Drozdowska
- School of Chemistry, Newcastle University Newcastle upon Tyne, UK
| | | | - Ralf Rabus
- Department of Microbiology, Max Planck Institute for Marine Microbiology Bremen, Germany ; General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment, Carl von Ossietzky University Oldenburg, Germany
| | - Heinz Wilkes
- Organic Geochemistry, Chemistry of the Earth, Helmholtz Centre Potsdam GFZ German Research Centre for Geosciences Potsdam, Germany ; Organic Geochemistry, Institute for Chemistry and Biology of the Marine Environment, Carl von Ossietzky University Oldenburg, Germany
| |
Collapse
|
12
|
Funk MA, Marsh ENG, Drennan CL. Substrate-bound structures of benzylsuccinate synthase reveal how toluene is activated in anaerobic hydrocarbon degradation. J Biol Chem 2015. [PMID: 26224635 DOI: 10.1074/jbc.m115.670737] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Various bacteria perform anaerobic degradation of small hydrocarbons as a source of energy and cellular carbon. To activate non-reactive hydrocarbons such as toluene, enzymes conjugate these molecules to fumarate in a radical-catalyzed, C-C bond-forming reaction. We have determined x-ray crystal structures of the glycyl radical enzyme that catalyzes the addition of toluene to fumarate, benzylsuccinate synthase (BSS), in two oligomeric states with fumarate alone or with both substrates. We find that fumarate is secured at the bottom of a long active site cavity with toluene bound directly above it. The two substrates adopt orientations that appear ideal for radical-mediated C-C bond formation; the methyl group of toluene is positioned between fumarate and a cysteine that forms a thiyl radical during catalysis, which is in turn adjacent to the glycine that serves as a radical storage residue. Toluene is held in place by fumarate on one face and tight packing by hydrophobic residues on the other face and sides. These hydrophobic residues appear to become ordered, thus encapsulating toluene, only in the presence of BSSβ, a small protein subunit that forms a tight complex with BSSα, the catalytic subunit. Enzymes related to BSS are able to metabolize a wide range of hydrocarbons through attachment to fumarate. Using our structures as a guide, we have constructed homology models of several of these "X-succinate synthases" and determined conservation patterns that will be useful in understanding the basis for catalysis and specificity in this family of enzymes.
Collapse
Affiliation(s)
| | - E Neil G Marsh
- the Department of Chemistry and Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109
| | - Catherine L Drennan
- From the Departments of Chemistry and Biology and the Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139 and
| |
Collapse
|
13
|
Structures of benzylsuccinate synthase elucidate roles of accessory subunits in glycyl radical enzyme activation and activity. Proc Natl Acad Sci U S A 2014; 111:10161-6. [PMID: 24982148 DOI: 10.1073/pnas.1405983111] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Anaerobic degradation of the environmental pollutant toluene is initiated by the glycyl radical enzyme benzylsuccinate synthase (BSS), which catalyzes the radical addition of toluene to fumarate, forming benzylsuccinate. We have determined crystal structures of the catalytic α-subunit of BSS with its accessory subunits β and γ, which both bind a [4Fe-4S] cluster and are essential for BSS activity in vivo. We find that BSSα has the common glycyl radical enzyme fold, a 10-stranded β/α-barrel that surrounds the glycyl radical cofactor and active site. Both accessory subunits β and γ display folds related to high potential iron-sulfur proteins but differ substantially from each other in how they interact with the α-subunit. BSSγ binds distally to the active site, burying a hydrophobic region of BSSα, whereas BSSβ binds to a hydrophilic surface of BSSα that is proximal to the active site. To further investigate the function of BSSβ, we determined the structure of a BSSαγ complex. Remarkably, we find that the barrel partially opens, allowing the C-terminal region of BSSα that houses the glycyl radical to shift within the barrel toward an exit pathway. The structural changes that we observe in the BSSαγ complex center around the crucial glycyl radical domain, thus suggesting a role for BSSβ in modulating the conformational dynamics required for enzyme activity. Accompanying proteolysis experiments support these structural observations.
Collapse
|
14
|
Boll M, Löffler C, Morris BEL, Kung JW. Anaerobic degradation of homocyclic aromatic compounds via arylcarboxyl-coenzyme A esters: organisms, strategies and key enzymes. Environ Microbiol 2013; 16:612-27. [PMID: 24238333 DOI: 10.1111/1462-2920.12328] [Citation(s) in RCA: 106] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Accepted: 11/03/2013] [Indexed: 11/28/2022]
Abstract
Next to carbohydrates, aromatic compounds are the second most abundant class of natural organic molecules in living organic matter but also make up a significant proportion of fossil carbon sources. Only microorganisms are capable of fully mineralizing aromatic compounds. While aerobic microbes use well-studied oxygenases for the activation and cleavage of aromatic rings, anaerobic bacteria follow completely different strategies to initiate catabolism. The key enzymes related to aromatic compound degradation in anaerobic bacteria are comprised of metal- and/or flavin-containing cofactors, of which many use unprecedented radical mechanisms for C-H bond cleavage or dearomatization. Over the past decade, the increasing number of completed genomes has helped to reveal a large variety of anaerobic degradation pathways in Proteobacteria, Gram-positive microbes and in one archaeon. This review aims to update our understanding of the occurrence of aromatic degradation capabilities in anaerobic microorganisms and serves to highlight characteristic enzymatic reactions involved in (i) the anoxic oxidation of alkyl side chains attached to aromatic rings, (ii) the carboxylation of aromatic rings and (iii) the reductive dearomatization of central arylcarboxyl-coenzyme A intermediates. Depending on the redox potential of the electron acceptors used and the metabolic efficiency of the cell, different strategies may be employed for identical overall reactions.
Collapse
Affiliation(s)
- Matthias Boll
- Institute for Biology II, University of Freiburg, Freiburg, Germany
| | | | | | | |
Collapse
|
15
|
Qrareya H, Ravelli D, Fagnoni M, Albini A. Decatungstate Photocatalyzed Benzylation of Alkenes with Alkylaromatics. Adv Synth Catal 2013. [DOI: 10.1002/adsc.201300598] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
|
16
|
Bharadwaj VS, Dean AM, Maupin CM. Insights into the Glycyl Radical Enzyme Active Site of Benzylsuccinate Synthase: A Computational Study. J Am Chem Soc 2013; 135:12279-88. [DOI: 10.1021/ja404842r] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Vivek S. Bharadwaj
- Chemical and Biological Engineering Department, Colorado School of Mines, 1500 Illinois Street, Golden,
Colorado 80401, United States
| | - Anthony M. Dean
- Chemical and Biological Engineering Department, Colorado School of Mines, 1500 Illinois Street, Golden,
Colorado 80401, United States
| | - C. Mark Maupin
- Chemical and Biological Engineering Department, Colorado School of Mines, 1500 Illinois Street, Golden,
Colorado 80401, United States
| |
Collapse
|
17
|
Li L. Mechanistic studies of the radical SAM enzyme spore photoproduct lyase (SPL). BIOCHIMICA ET BIOPHYSICA ACTA 2012; 1824:1264-77. [PMID: 22197590 PMCID: PMC3314140 DOI: 10.1016/j.bbapap.2011.11.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2011] [Accepted: 11/28/2011] [Indexed: 02/06/2023]
Abstract
Spore photoproduct lyase (SPL) repairs a special thymine dimer 5-thyminyl-5,6-dihydrothymine, which is commonly called spore photoproduct or SP at the bacterial early germination phase. SP is the exclusive DNA photo-damage product in bacterial endospores; its generation and swift repair by SPL are responsible for the spores' extremely high UV resistance. The early in vivo studies suggested that SPL utilizes a direct reversal strategy to repair the SP in the absence of light. The research in the past decade further established SPL as a radical SAM enzyme, which utilizes a tri-cysteine CXXXCXXC motif to harbor a [4Fe-4S] cluster. At the 1+ oxidation state, the cluster provides an electron to the S-adenosylmethionine (SAM), which binds to the cluster in a bidentate manner as the fourth and fifth ligands, to reductively cleave the CS bond associated with the sulfonium ion in SAM, generating a reactive 5'-deoxyadenosyl (5'-dA) radical. This 5'-dA radical abstracts the proR hydrogen atom from the C6 carbon of SP to initiate the repair process; the resulting SP radical subsequently fragments to generate a putative thymine methyl radical, which accepts a back-donated H atom to yield the repaired TpT. SAM is suggested to be regenerated at the end of each catalytic cycle; and only a catalytic amount of SAM is needed in the SPL reaction. The H atom source for the back donation step is suggested to be a cysteine residue (C141 in Bacillus subtilis SPL), and the H-atom transfer reaction leaves a thiyl radical behind on the protein. This thiyl radical thus must participate in the SAM regeneration process; however how the thiyl radical abstracts an H atom from the 5'-dA to regenerate SAM is unknown. This paper reviews and discusses the history and the latest progress in the mechanistic elucidation of SPL. Despite some recent breakthroughs, more questions are raised in the mechanistic understanding of this intriguing DNA repair enzyme. This article is part of a Special Issue entitled: Radical SAM enzymes and Radical Enzymology.
Collapse
Affiliation(s)
- Lei Li
- Department of Chemistry, Indiana University-Purdue University Indianapolis (IUPUI), 402 N Blackford Street, Indianapolis, IN 46202, USA.
| |
Collapse
|
18
|
Lanz ND, Booker SJ. Identification and function of auxiliary iron-sulfur clusters in radical SAM enzymes. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2012; 1824:1196-212. [PMID: 22846545 DOI: 10.1016/j.bbapap.2012.07.009] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2012] [Revised: 07/16/2012] [Accepted: 07/17/2012] [Indexed: 11/27/2022]
Abstract
Radical SAM (RS) enzymes use a 5'-deoxyadenosyl 5'-radical generated from a reductive cleavage of S-adenosyl-l-methionine to catalyze over 40 distinct reaction types. A distinguishing feature of these enzymes is a [4Fe-4S] cluster to which each of three iron ions is ligated by three cysteinyl residues most often located in a Cx(3)Cx(2)C motif. The α-amino and α-carboxylate groups of SAM anchor the molecule to the remaining iron ion, which presumably facilitates its reductive cleavage. A subset of RS enzymes contains additional iron-sulfur clusters, - which we term auxiliary clusters - most of which have unidentified functions. Enzymes in this subset are involved in cofactor biosynthesis and maturation, post-transcriptional and post-translational modification, enzyme activation, and antibiotic biosynthesis. The additional clusters in these enzymes have been proposed to function in sulfur donation, electron transfer, and substrate anchoring. This review will highlight evidence supporting the presence of multiple iron-sulfur clusters in these enzymes as well as their predicted roles in catalysis. This article is part of a special issue entitled: Radical SAM enzymes and radical enzymology.
Collapse
Affiliation(s)
- Nicholas D Lanz
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | | |
Collapse
|
19
|
Marsh ENG, Patterson DP, Li L. Adenosyl radical: reagent and catalyst in enzyme reactions. Chembiochem 2010; 11:604-21. [PMID: 20191656 PMCID: PMC3011887 DOI: 10.1002/cbic.200900777] [Citation(s) in RCA: 88] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2009] [Indexed: 12/17/2022]
Abstract
Adenosine is undoubtedly an ancient biological molecule that is a component of many enzyme cofactors: ATP, FADH, NAD(P)H, and coenzyme A, to name but a few, and, of course, of RNA. Here we present an overview of the role of adenosine in its most reactive form: as an organic radical formed either by homolytic cleavage of adenosylcobalamin (coenzyme B(12), AdoCbl) or by single-electron reduction of S-adenosylmethionine (AdoMet) complexed to an iron-sulfur cluster. Although many of the enzymes we discuss are newly discovered, adenosine's role as a radical cofactor most likely arose very early in evolution, before the advent of photosynthesis and the production of molecular oxygen, which rapidly inactivates many radical enzymes. AdoCbl-dependent enzymes appear to be confined to a rather narrow repertoire of rearrangement reactions involving 1,2-hydrogen atom migrations; nevertheless, mechanistic insights gained from studying these enzymes have proved extremely valuable in understanding how enzymes generate and control highly reactive free radical intermediates. In contrast, there has been a recent explosion in the number of radical-AdoMet enzymes discovered that catalyze a remarkably wide range of chemically challenging reactions; here there is much still to learn about their mechanisms. Although all the radical-AdoMet enzymes so far characterized come from anaerobically growing microbes and are very oxygen sensitive, there is tantalizing evidence that some of these enzymes might be active in aerobic organisms including humans.
Collapse
Affiliation(s)
- E. Neil G. Marsh
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA
| | - Dustin P. Patterson
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA
| | - Lei Li
- Department of Chemistry and Chemical Biology, Indiana University – Purdue University Indianapolis, Indianapolis, IN 46202, USA
| |
Collapse
|
20
|
Abstract
An increasing number of enzymes are being discovered that contain radicals or catalyze reactions via radical intermediates. These radical enzymes are able to open reaction pathways that two-electron steps cannot achieve. Recently, organic chemists started to apply related radical chemistry for synthetic purposes, whereby an electron energized by light is recycled in every turnover. This Minireview compares this new type of reaction with enzymes that use recycling radicals and single electrons as cofactors.
Collapse
Affiliation(s)
- Wolfgang Buckel
- Laboratorium für Mikrobiologie, Fachbereich Biologie, Philipps-Universität, 35032 Marburg, Germany.
| |
Collapse
|
21
|
Herrmann S, Vogt C, Fischer A, Kuppardt A, Richnow HH. Characterization of anaerobic xylene biodegradation by two-dimensional isotope fractionation analysis. ENVIRONMENTAL MICROBIOLOGY REPORTS 2009; 1:535-544. [PMID: 23765932 DOI: 10.1111/j.1758-2229.2009.00076.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
We determined stable carbon and hydrogen isotope fractionation factors for anaerobic degradation of xylene isomers by several pure and mixed cultures. All cultures initiated xylene degradation by the addition of fumarate to a methyl moiety, as is known from the literature or verified by the presence of methylbenzylsuccinates as metabolic intermediates. Additionally, the A subunit of benzylsuccinate synthase (bssA) was identified in the majority of the cultures by bssA-targeted primers. Xylene degradation was always coupled to a significant carbon and hydrogen isotope fractionation. The values of the apparent kinetic isotope effect (AKIE) for carbon and hydrogen indicate that the cleavage of a carbon-hydrogen bond is an isotope-sensitive step during fumarate addition to xylene isomers. The slopes of the linear regression for hydrogen (Δδ(2) H) versus carbon (Δδ(13) C) discrimination (Λ = Δδ(2) H/Δδ(13) C ≈ εHbulk /εCbulk ) ranged from 12 ± 4 to 29 ± 5 and were comparable to Λ values previously determined for anaerobic toluene degradation. The results suggest that combined carbon and hydrogen isotope fractionation analyses can be used to monitor anaerobic xylene degradation at contaminated sites.
Collapse
Affiliation(s)
- Steffi Herrmann
- Departments of Isotope Biogeochemistry and Environmental Microbiology, UFZ - Helmholtz Centre for Environmental Research, Leipzig, Germany. Isodetect - Company for Isotope Monitoring, Leipzig, Munich, Germany
| | | | | | | | | |
Collapse
|
22
|
|
23
|
Li L, Patterson DP, Fox CC, Lin B, Coschigano PW, Marsh ENG. Subunit structure of benzylsuccinate synthase. Biochemistry 2009; 48:1284-92. [PMID: 19159265 DOI: 10.1021/bi801766g] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Benzylsuccinate synthase is a member of the glycyl radical family of enzymes. It catalyzes the addition of toluene to fumarate to form benzylsuccinate as the first step in the anaerobic pathway of toluene fermentation. The enzyme comprises three subunits, alpha, beta, and gamma, that in Thauera aromatica strain T1 are encoded by the tutD, tutG, and tutF genes, respectively. The large alpha-subunit contains the essential glycine and cysteine residues that are conserved in all glycyl radical enzymes. However, the function of the small beta- and gamma-subunits has remained unclear. We have overexpressed all three subunits of benzylsuccinate synthase in Escherichia coli, both individually and in combination. Coexpression of the gamma-subunit (but not the beta-subunit) is essential for efficient expression of the alpha-subunit. The benzylsuccinate synthase complex lacking the glycyl radical could be purified as an alpha(2)beta(2)gamma(2) hexamer by nickel affinity chromatography through a "His(6)" affinity tag engineered onto the C-terminus of the alpha-subunit. Unexpectedly, BSS was found to contain two iron-sulfur clusters, one associated with the beta-subunit and the other with the gamma-subunit that appear to be necessary for the structural integrity of the complex. The spectroscopic properties of these clusters suggest that they are most likely [4Fe-4S] clusters. Removal of iron with chelating agents results in dissociation of the complex; similarly, a mutant gamma-subunit lacking the [4Fe-4S] cluster is unable to stabilize the alpha-subunit when the proteins are coexpressed.
Collapse
Affiliation(s)
- Lei Li
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109-1055, USA
| | | | | | | | | | | |
Collapse
|
24
|
Insights into the mechanisms of adenosylcobalamin (coenzyme B12)-dependent enzymes from rapid chemical quench experiments. Biochem Soc Trans 2009; 37:336-42. [PMID: 19290858 DOI: 10.1042/bst0370336] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Glutamate mutase is one of a group of adenosylcobalamin-dependent enzymes that use free radicals to catalyse unusual and chemically difficult rearrangements involving 1,2-migrations of hydrogen atoms. A key mechanistic feature of these enzymes is the transfer of the migrating hydrogen atom between substrate, coenzyme and product. The present review summarizes recent experiments from my laboratory that have used rapid chemical quench techniques to identify intermediates in the reaction and probe the mechanism of hydrogen transfer through a variety of pre-steady-state kinetic isotope effect measurements.
Collapse
|
25
|
Abstract
Methane has long been known to be used as a carbon and energy source by some aerobic alpha- and delta-proteobacteria. In these organisms the metabolism of methane starts with its oxidation with O(2) to methanol, a reaction catalyzed by a monooxygenase and therefore restricted to the aerobic world. Methane has recently been shown to also fuel the growth of anaerobic microorganisms. The oxidation of methane with sulfate and with nitrate have been reported, but the mechanisms of anaerobic methane oxidation still remains elusive. Sulfate-dependent methane oxidation is catalyzed by methanotrophic archaea, which are related to the Methanosarcinales and which grow in close association with sulfate-reducing delta-proteobacteria. There is evidence that anaerobic methane oxidation with sulfate proceeds at least in part via reversed methanogenesis involving the nickel enzyme methyl-coenzyme M reductase for methane activation, which under standard conditions is an endergonic reaction, and thus inherently slow. Methane oxidation coupled to denitrification is mediated by bacteria belonging to a novel phylum and does not involve methyl-coenzyme M reductase. The first step in methane oxidation is most likely the exergonic formation of 2-methylsuccinate from fumarate and methane catalyzed by a glycine-radical enzyme.
Collapse
Affiliation(s)
- Rudolf K Thauer
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Strasse, D-35043 Marburg, Germany.
| | | |
Collapse
|
26
|
Shi FQ, Li X, Xia Y, Zhang L, Yu ZX. DFT Study of the Mechanisms of In Water Au(I)-Catalyzed Tandem [3,3]-Rearrangement/Nazarov Reaction/[1,2]-Hydrogen Shift of Enynyl Acetates: A Proton-Transport Catalysis Strategy in the Water-Catalyzed [1,2]-Hydrogen Shift. J Am Chem Soc 2007; 129:15503-12. [DOI: 10.1021/ja071070+] [Citation(s) in RCA: 266] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|