1
|
Szaleniec M, Oleksy G, Sekuła A, Aleksić I, Pietras R, Sarewicz M, Krämer K, Pierik AJ, Heider J. Modeling the Initiation Phase of the Catalytic Cycle in the Glycyl-Radical Enzyme Benzylsuccinate Synthase. J Phys Chem B 2024; 128:5823-5839. [PMID: 38848492 PMCID: PMC11194802 DOI: 10.1021/acs.jpcb.4c01237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 05/15/2024] [Accepted: 05/16/2024] [Indexed: 06/09/2024]
Abstract
The reaction of benzylsuccinate synthase, the radical-based addition of toluene to a fumarate cosubstrate, is initiated by hydrogen transfer from a conserved cysteine to the nearby glycyl radical in the active center of the enzyme. In this study, we analyze this step by comprehensive computer modeling, predicting (i) the influence of bound substrates or products, (ii) the energy profiles of forward- and backward hydrogen-transfer reactions, (iii) their kinetic constants and potential mechanisms, (iv) enantiospecificity differences, and (v) kinetic isotope effects. Moreover, we support several of the computational predictions experimentally, providing evidence for the predicted H/D-exchange reactions into the product and at the glycyl radical site. Our data indicate that the hydrogen transfer reactions between the active site glycyl and cysteine are principally reversible, but their rates differ strongly depending on their stereochemical orientation, transfer of protium or deuterium, and the presence or absence of substrates or products in the active site. This is particularly evident for the isotope exchange of the remaining protium atom of the glycyl radical to deuterium, which appears dependent on substrate or product binding, explaining why the exchange is observed in some, but not all, glycyl-radical enzymes.
Collapse
Affiliation(s)
- Maciej Szaleniec
- Jerzy
Haber Institute of Catalysis and Surface Chemistry, Polish Academy
of Sciences, Kraków 31-201, Poland
| | - Gabriela Oleksy
- Jerzy
Haber Institute of Catalysis and Surface Chemistry, Polish Academy
of Sciences, Kraków 31-201, Poland
- Department
of Biology, Laboratory for Microbial Biochemistry, Philipps University Marburg, Marburg 35043, Germany
| | - Anna Sekuła
- Jerzy
Haber Institute of Catalysis and Surface Chemistry, Polish Academy
of Sciences, Kraków 31-201, Poland
| | - Ivana Aleksić
- Jerzy
Haber Institute of Catalysis and Surface Chemistry, Polish Academy
of Sciences, Kraków 31-201, Poland
| | - Rafał Pietras
- Department
of Molecular Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków 31-007, Poland
| | - Marcin Sarewicz
- Department
of Molecular Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków 31-007, Poland
| | - Kai Krämer
- Department
of Biology, Laboratory for Microbial Biochemistry, Philipps University Marburg, Marburg 35043, Germany
| | - Antonio J. Pierik
- Biochemistry,
Faculty of ChemistryRPTU Kaiserslautern-Landau, Kaiserslautern D-67663, Germany
| | - Johann Heider
- Department
of Biology, Laboratory for Microbial Biochemistry, Philipps University Marburg, Marburg 35043, Germany
- Synmikro-Center
for Synthetic Microbiology, Philipps University
Marburg, Marburg 35043, Germany
| |
Collapse
|
2
|
Semenya J, Yang Y, Picazo E. Cross-Electrophile Coupling of Benzyl Halides and Disulfides Catalyzed by Iron. J Am Chem Soc 2024; 146:4903-4912. [PMID: 38346333 PMCID: PMC10910570 DOI: 10.1021/jacs.3c13984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 01/22/2024] [Accepted: 01/24/2024] [Indexed: 02/22/2024]
Abstract
Cross-electrophile couplings are influential reactions that typically require a terminal reductant or photoredox conditions. We discovered an iron-catalyzed reaction that couples benzyl halides with disulfides to yield thioether products in the absence of a terminal reductant and under photoredox conditions. The disclosed platform proceeds without sulfur-induced catalyst poisoning or the use of an exogenous base, supporting a broad scope and circumventing undesired elimination pathways. We applied the developed chemistry in a new mode of disulfide bioconjugation, drug synthesis, gram-scale synthesis, and product derivatization. Lastly, we performed mechanistic experiments to better understand the stereoablative reaction between two electrophiles. Disulfides and benzylic thioethers are imperative for biological and pharmaceutical applications but remain severely understudied in comparison to their ethereal and amino counterparts. Hence, we expect this platform of iron catalysis and the downstream applications to be of interest to the greater scientific community.
Collapse
Affiliation(s)
- Julius Semenya
- Department of Chemistry, Loker Hydrocarbon Research Institute, University of
Southern California, 837 Bloom Walk, Los Angeles, California 90089-1661, United States
| | - Yuanjie Yang
- Department of Chemistry, Loker Hydrocarbon Research Institute, University of
Southern California, 837 Bloom Walk, Los Angeles, California 90089-1661, United States
| | - Elias Picazo
- Department of Chemistry, Loker Hydrocarbon Research Institute, University of
Southern California, 837 Bloom Walk, Los Angeles, California 90089-1661, United States
| |
Collapse
|
3
|
Casini I, McCubbin T, Esquivel-Elizondo S, Luque GG, Evseeva D, Fink C, Beblawy S, Youngblut ND, Aristilde L, Huson DH, Dräger A, Ley RE, Marcellin E, Angenent LT, Molitor B. An integrated systems biology approach reveals differences in formate metabolism in the genus Methanothermobacter. iScience 2023; 26:108016. [PMID: 37854702 PMCID: PMC10579436 DOI: 10.1016/j.isci.2023.108016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 08/29/2023] [Accepted: 09/19/2023] [Indexed: 10/20/2023] Open
Abstract
Methanogenesis allows methanogenic archaea to generate cellular energy for their growth while producing methane. Thermophilic hydrogenotrophic species of the genus Methanothermobacter have been recognized as robust biocatalysts for a circular carbon economy and are already applied in power-to-gas technology with biomethanation, which is a platform to store renewable energy and utilize captured carbon dioxide. Here, we generated curated genome-scale metabolic reconstructions for three Methanothermobacter strains and investigated differences in the growth performance of these same strains in chemostat bioreactor experiments with hydrogen and carbon dioxide or formate as substrates. Using an integrated systems biology approach, we identified differences in formate anabolism between the strains and revealed that formate anabolism influences the diversion of carbon between biomass and methane. This finding, together with the omics datasets and the metabolic models we generated, can be implemented for biotechnological applications of Methanothermobacter in power-to-gas technology, and as a perspective, for value-added chemical production.
Collapse
Affiliation(s)
- Isabella Casini
- Environmental Biotechnology Group, Department of Geosciences, University of Tübingen, Schnarrenbergstraße 94-96, 72076 Tübingen, Germany
| | - Tim McCubbin
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD 4072, Australia
- Queensland Metabolomics and Proteomics (Q-MAP), The University of Queensland, Brisbane, QLD 4072, Australia
- ARC Centre of Excellence in Synthetic Biology (COESB), The University of Queensland, Brisbane, QLD 4072, Australia
| | - Sofia Esquivel-Elizondo
- Department of Microbiome Science, Max Planck Institute for Biology Tübingen, Max-Planck-Ring 5, 72076 Tübingen, Germany
| | - Guillermo G. Luque
- Department of Microbiome Science, Max Planck Institute for Biology Tübingen, Max-Planck-Ring 5, 72076 Tübingen, Germany
| | - Daria Evseeva
- Department of Computer Science, University of Tübingen, Sand 14, 72076 Tübingen, Germany
- Institute for Bioinformatics and Medical Informatics (IBMI), University of Tübingen, 72076 Tübingen, Germany
| | - Christian Fink
- Environmental Biotechnology Group, Department of Geosciences, University of Tübingen, Schnarrenbergstraße 94-96, 72076 Tübingen, Germany
| | - Sebastian Beblawy
- Environmental Biotechnology Group, Department of Geosciences, University of Tübingen, Schnarrenbergstraße 94-96, 72076 Tübingen, Germany
| | - Nicholas D. Youngblut
- Department of Microbiome Science, Max Planck Institute for Biology Tübingen, Max-Planck-Ring 5, 72076 Tübingen, Germany
| | - Ludmilla Aristilde
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, IL 60208, USA
| | - Daniel H. Huson
- Department of Computer Science, University of Tübingen, Sand 14, 72076 Tübingen, Germany
- Institute for Bioinformatics and Medical Informatics (IBMI), University of Tübingen, 72076 Tübingen, Germany
- Cluster of Excellence – Controlling Microbes to Fight Infections, University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany
| | - Andreas Dräger
- Department of Computer Science, University of Tübingen, Sand 14, 72076 Tübingen, Germany
- Institute for Bioinformatics and Medical Informatics (IBMI), University of Tübingen, 72076 Tübingen, Germany
- Cluster of Excellence – Controlling Microbes to Fight Infections, University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany
| | - Ruth E. Ley
- Department of Microbiome Science, Max Planck Institute for Biology Tübingen, Max-Planck-Ring 5, 72076 Tübingen, Germany
- Cluster of Excellence – Controlling Microbes to Fight Infections, University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany
| | - Esteban Marcellin
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD 4072, Australia
- Queensland Metabolomics and Proteomics (Q-MAP), The University of Queensland, Brisbane, QLD 4072, Australia
- ARC Centre of Excellence in Synthetic Biology (COESB), The University of Queensland, Brisbane, QLD 4072, Australia
| | - Largus T. Angenent
- Environmental Biotechnology Group, Department of Geosciences, University of Tübingen, Schnarrenbergstraße 94-96, 72076 Tübingen, Germany
- Cluster of Excellence – Controlling Microbes to Fight Infections, University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany
- AG Angenent, Max Planck Institute for Biology Tübingen, Max-Planck-Ring 5, 72076 Tübingen, Germany
- Department of Biological and Chemical Engineering, Aarhus University, Gustav Wieds Vej 10D, 8000 Aarhus C, Denmark
- The Novo Nordisk Foundation CO2 Research Center (CORC), Aarhus University, Gustav Wieds Vej 10C, 8000 Aarhus C, Denmark
| | - Bastian Molitor
- Environmental Biotechnology Group, Department of Geosciences, University of Tübingen, Schnarrenbergstraße 94-96, 72076 Tübingen, Germany
- Cluster of Excellence – Controlling Microbes to Fight Infections, University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany
| |
Collapse
|
4
|
Fietze T, Wilk P, Kabinger F, Anoosheh S, Hofer A, Lundin D, Feiler CG, Weiss MS, Loderer C. HUG Domain Is Responsible for Active Dimer Stabilization in an NrdJd Ribonucleotide Reductase. Biochemistry 2022; 61:1633-1641. [PMID: 35856337 DOI: 10.1021/acs.biochem.2c00173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Ribonucleotide reductases (RNRs) catalyze the reduction of ribonucleotides to the corresponding deoxyribonucleotides. The catalytic activity of most RNRs depends on the formation of a dimer of the catalytic subunits. The active site is located at the interface, and part of the substrate binding site and regulatory mechanisms work across the subunit in the dimer. In this study, we describe and characterize a novel domain responsible for forming the catalytic dimer in several class II RNRs. The 3D structure of the class II RNR from Rhodobacter sphaeroides reveals a so far undescribed α-helical domain in the dimer interface, which is embracing the other subunit. Genetic removal of this HUG domain leads to a severe reduction of activity paired with reduced dimerization capability. In comparison with other described RNRs, the enzyme with this domain is less dependent on the presence of nucleotides to act as allosteric effectors in the formation of dimers. The HUG domain appears to serve as an interlock to keep the dimer intact and functional even at low enzyme and/or effector concentrations.
Collapse
Affiliation(s)
- Tobias Fietze
- Chair of Molecular Biotechnology, Technische Universität Dresden, Dresden 01217, Germany
| | - Piotr Wilk
- Macromolecular Crystallography, Helmholtz-Zentrum Berlin, Berlin 12489, Germany.,Malopolska Centre of Biotechnology (MCB), Jagiellonian University, Krakow 31-007, Poland
| | - Florian Kabinger
- Department of Molecular Biology, Max Planck Institute for Multidisciplinary Sciences, Göttingen 37077, Germany
| | - Saber Anoosheh
- Department of Medical Biochemistry, Umeå University, Umeå 1965, Sweden
| | - Anders Hofer
- Department of Medical Biochemistry, Umeå University, Umeå 1965, Sweden
| | - Daniel Lundin
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm 114 19, Sweden
| | - Christian G Feiler
- Macromolecular Crystallography, Helmholtz-Zentrum Berlin, Berlin 12489, Germany
| | - Manfred S Weiss
- Macromolecular Crystallography, Helmholtz-Zentrum Berlin, Berlin 12489, Germany
| | - Christoph Loderer
- Chair of Molecular Biotechnology, Technische Universität Dresden, Dresden 01217, Germany
| |
Collapse
|
5
|
Levitz TS, Andree GA, Jonnalagadda R, Dawson CD, Bjork RE, Drennan CL. A rapid and sensitive assay for quantifying the activity of both aerobic and anaerobic ribonucleotide reductases acting upon any or all substrates. PLoS One 2022; 17:e0269572. [PMID: 35675376 PMCID: PMC9176816 DOI: 10.1371/journal.pone.0269572] [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] [Received: 02/07/2022] [Accepted: 05/23/2022] [Indexed: 01/21/2023] Open
Abstract
Ribonucleotide reductases (RNRs) use radical-based chemistry to catalyze the conversion of all four ribonucleotides to deoxyribonucleotides. The ubiquitous nature of RNRs necessitates multiple RNR classes that differ from each other in terms of the phosphorylation state of the ribonucleotide substrates, oxygen tolerance, and the nature of both the metallocofactor employed and the reducing systems. Although these differences allow RNRs to produce deoxyribonucleotides needed for DNA biosynthesis under a wide range of environmental conditions, they also present a challenge for establishment of a universal activity assay. Additionally, many current RNR assays are limited in that they only follow the conversion of one ribonucleotide substrate at a time, but in the cell, all four ribonucleotides are actively being converted into deoxyribonucleotide products as dictated by the cellular concentrations of allosteric specificity effectors. Here, we present a liquid chromatography with tandem mass spectrometry (LC-MS/MS)-based assay that can determine the activity of both aerobic and anaerobic RNRs on any combination of substrates using any combination of allosteric effectors. We demonstrate that this assay generates activity data similar to past published results with the canonical Escherichia coli aerobic class Ia RNR. We also show that this assay can be used for an anaerobic class III RNR that employs formate as the reductant, i.e. Streptococcus thermophilus RNR. We further show that this class III RNR is allosterically regulated by dATP and ATP. Lastly, we present activity data for the simultaneous reduction of all four ribonucleotide substrates by the E. coli class Ia RNR under various combinations of allosteric specificity effectors. This validated LC-MS/MS assay is higher throughput and more versatile than the historically established radioactive activity and coupled RNR activity assays as well as a number of the published HPLC-based assays. The presented assay will allow for the study of a wide range of RNR enzymes under a wide range of conditions, facilitating the study of previously uncharacterized RNRs.
Collapse
Affiliation(s)
- Talya S. Levitz
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, United States of America
| | - Gisele A. Andree
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, United States of America
| | - Rohan Jonnalagadda
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, United States of America
| | - Christopher D. Dawson
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, United States of America
| | - Rebekah E. Bjork
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, United States of America
| | - Catherine L. Drennan
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, United States of America,Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, United States of America,Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, United States of America,Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA, United States of America,* E-mail:
| |
Collapse
|
6
|
Structural Insights into a Fusion Protein between a Glutaredoxin-like and a Ferredoxin-Disulfide Reductase Domain from an Extremophile Bacterium. INORGANICS 2022. [DOI: 10.3390/inorganics10020024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
In eukaryotic photosynthetic organisms, ferredoxin–thioredoxin reductases (FTRs) are key proteins reducing several types of chloroplastic thioredoxins (TRXs) in light conditions. The electron cascade necessary to reduce oxidized TRXs involves a pair of catalytic cysteines and a [4Fe–4S] cluster present at the level of the FTR catalytic subunit, the iron–sulfur cluster receiving electrons from ferredoxins. Genomic analyses revealed the existence of FTR orthologs in non-photosynthetic organisms, including bacteria and archaea, referred to as ferredoxin-disulfide reductase (FDR) as they reduce various types of redoxins. In this study, we describe the tridimensional structure of a natural hybrid protein formed by an N-terminal glutaredoxin-like domain fused to a FDR domain present in the marine bacterium Desulfotalea psychrophila Lsv54. This structure provides information on how and why the absence of the variable subunit present in FTR heterodimer which normally protects the Fe–S cluster is dispensable in FDR proteins. In addition, modelling of a tripartite complex based on the existing structure of a rubredoxin (RBX)–FDR fusion present in anaerobic methanogen archaea allows recapitulating the electron flow involving these RBX, FDR and GRX protein domains.
Collapse
|
7
|
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
|
8
|
Schell E, Nouairia G, Steiner E, Weber N, Lundin D, Loderer C. Structural determinants and distribution of phosphate specificity in ribonucleotide reductases. J Biol Chem 2021; 297:101008. [PMID: 34314684 PMCID: PMC8365446 DOI: 10.1016/j.jbc.2021.101008] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 07/21/2021] [Accepted: 07/23/2021] [Indexed: 11/24/2022] Open
Abstract
Ribonucleotide reductases (RNRs) catalyze the reduction of ribonucleotides to the corresponding deoxyribonucleotides, the building blocks of DNA. RNRs are specific for either ribonucleoside diphosphates or triphosphates as substrates. As far as is known, oxygen-dependent class I RNRs (NrdAB) all reduce ribonucleoside diphosphates, and oxygen-sensitive class III RNRs (NrdD) are all ribonucleoside triphosphate reducers, whereas the adenosylcobalamin-dependent class II (NrdJ) contains both ribonucleoside diphosphate and triphosphate reducers. However, it is unknown how this specificity is conveyed by the active site of the enzymes and how this feature developed in RNR evolution. By structural comparison of the active sites in different RNRs, we identified the apical loop of the phosphate-binding site as a potential structural determinant of substrate specificity. Grafting two residues from this loop from a diphosphate- to a triphosphate-specific RNR caused a change in preference from ribonucleoside triphosphate to diphosphate substrates in a class II model enzyme, confirming them as the structural determinants of phosphate specificity. The investigation of the phylogenetic distribution of this motif in class II RNRs yielded a likely monophyletic clade with the diphosphate-defining motif. This indicates a single evolutionary-split event early in NrdJ evolution in which diphosphate specificity developed from the earlier triphosphate specificity. For those interesting cases where organisms contain more than one nrdJ gene, we observed a preference for encoding enzymes with diverse phosphate specificities, suggesting that this varying phosphate specificity confers a selective advantage.
Collapse
Affiliation(s)
- Eugen Schell
- Institute for Microbiology, Technische Universität Dresden, Dresden, Saxony, Germany
| | - Ghada Nouairia
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Elisabeth Steiner
- Institute for Microbiology, Technische Universität Dresden, Dresden, Saxony, Germany
| | - Niclas Weber
- Institute for Microbiology, Technische Universität Dresden, Dresden, Saxony, Germany
| | - Daniel Lundin
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Christoph Loderer
- Institute for Microbiology, Technische Universität Dresden, Dresden, Saxony, Germany.
| |
Collapse
|
9
|
A ferredoxin-dependent dihydropyrimidine dehydrogenase in Clostridium chromiireducens. Biosci Rep 2020; 40:225330. [PMID: 32614053 PMCID: PMC7332683 DOI: 10.1042/bsr20201642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 06/05/2020] [Accepted: 06/09/2020] [Indexed: 11/21/2022] Open
Abstract
Dihydropyrimidine dehydrogenase (PydA) catalyzes the first step of the reductive pyrimidine degradation (Pyd) pathway in bacteria and eukaryotes, enabling pyrimidines to be utilized as substrates for growth. PydA homologs studied to date catalyze the reduction of uracil to dihydrouracil, coupled to the oxidation of NAD(P)H. Uracil reduction occurs at a flavin mononucleotide (FMN) site, and NAD(P)H oxidation occurs at a flavin adenine dinucleotide (FAD) site, with two ferredoxin domains thought to mediate inter-site electron transfer. Here, we report the biochemical characterization of a Clostridial PydA homolog (PydAc) from a Pyd gene cluster in the strict anaerobic bacterium Clostridium chromiireducens. PydAc lacks the FAD domain, and instead is able to catalyze uracil reduction using reduced methyl viologen or reduced ferredoxin as the electron source. Homologs of PydAc are present in Pyd gene clusters in many strict anaerobic bacteria, which use reduced ferredoxin as an intermediate in their energy metabolism.
Collapse
|
10
|
Gumkowski JD, Martinie RJ, Corrigan PS, Pan J, Bauerle MR, Almarei M, Booker SJ, Silakov A, Krebs C, Boal AK. Analysis of RNA Methylation by Phylogenetically Diverse Cfr Radical S-Adenosylmethionine Enzymes Reveals an Iron-Binding Accessory Domain in a Clostridial Enzyme. Biochemistry 2019; 58:3169-3184. [PMID: 31246421 DOI: 10.1021/acs.biochem.9b00197] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Cfr is a radical S-adenosylmethionine (SAM) RNA methylase linked to multidrug antibiotic resistance in bacterial pathogens. It catalyzes a chemically challenging C-C bond-forming reaction to methylate C8 of A2503 (Escherichia coli numbering) of 23S rRNA during ribosome assembly. The cfr gene has been identified as a mobile genetic element in diverse bacteria and in the genome of select Bacillales and Clostridiales species. Despite the importance of Cfr, few representatives have been purified and characterized in vitro. Here we show that Cfr homologues from Bacillus amyloliquefaciens, Enterococcus faecalis, Paenibacillus lautus, and Clostridioides difficile act as C8 adenine RNA methylases in biochemical assays. C. difficile Cfr contains an additional Cys-rich C-terminal domain that binds a mononuclear Fe2+ ion in a rubredoxin-type Cys4 motif. The C-terminal domain can be truncated with minimal impact on C. difficile Cfr activity, but the rate of turnover is decreased upon disruption of the Fe2+-binding site by Zn2+ substitution or ligand mutation. These findings indicate an important purpose for the observed C-terminal iron in the native fusion protein. Bioinformatic analysis of the C. difficile Cfr Cys-rich domain shows that it is widespread (∼1400 homologues) as a stand-alone gene in pathogenic or commensal Bacilli and Clostridia, with >10% encoded adjacent to a predicted radical SAM RNA methylase. Although the domain is not essential for in vitro C. difficile Cfr activity, the genomic co-occurrence and high abundance in the human microbiome suggest a possible functional role for a specialized rubredoxin in certain radical SAM RNA methylases that are relevant to human health.
Collapse
Affiliation(s)
- James D Gumkowski
- Department of Chemistry , The Pennsylvania State University , University Park , Pennsylvania 16802 , United States
| | - Ryan J Martinie
- Department of Chemistry , The Pennsylvania State University , University Park , Pennsylvania 16802 , United States
| | - Patrick S Corrigan
- Department of Chemistry , The Pennsylvania State University , University Park , Pennsylvania 16802 , United States
| | - Juan Pan
- Department of Chemistry , The Pennsylvania State University , University Park , Pennsylvania 16802 , United States
| | - Matthew R Bauerle
- Department of Chemistry , The Pennsylvania State University , University Park , Pennsylvania 16802 , United States
| | - Mohamed Almarei
- Department of Biochemistry and Molecular Biology , The Pennsylvania State University , University Park , Pennsylvania 16802 , United States
| | - Squire J Booker
- Department of Chemistry , The Pennsylvania State University , University Park , Pennsylvania 16802 , United States.,Department of Biochemistry and Molecular Biology , The Pennsylvania State University , University Park , Pennsylvania 16802 , United States.,Howard Hughes Medical Institute , The Pennsylvania State University , University Park , Pennsylvania 16802 , United States
| | - Alexey Silakov
- Department of Chemistry , The Pennsylvania State University , University Park , Pennsylvania 16802 , United States
| | - Carsten Krebs
- Department of Chemistry , The Pennsylvania State University , University Park , Pennsylvania 16802 , United States.,Department of Biochemistry and Molecular Biology , The Pennsylvania State University , University Park , Pennsylvania 16802 , United States
| | - Amie K Boal
- Department of Chemistry , The Pennsylvania State University , University Park , Pennsylvania 16802 , United States.,Department of Biochemistry and Molecular Biology , The Pennsylvania State University , University Park , Pennsylvania 16802 , United States
| |
Collapse
|
11
|
Loderer C, Holmfeldt K, Lundin D. Non-host class II ribonucleotide reductase in Thermus viruses: sequence adaptation and host interaction. PeerJ 2019; 7:e6700. [PMID: 30993041 PMCID: PMC6459318 DOI: 10.7717/peerj.6700] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Accepted: 03/01/2019] [Indexed: 01/14/2023] Open
Abstract
Ribonucleotide reductases (RNR) are essential enzymes for all known life forms. Their current taxonomic distribution suggests extensive horizontal gene transfer e.g., by processes involving viruses. To improve our understanding of the underlying processes, we characterized a monomeric class II RNR (NrdJm) enzyme from a Thermus virus, a subclass not present in any sequenced Thermus spp. genome. Phylogenetic analysis revealed a distant origin of the nrdJm gene with the most closely related sequences found in mesophiles or moderate thermophiles from the Firmicutes phylum. GC-content, codon usage and the ratio of coding to non-coding substitutions (dN/dS) suggest extensive adaptation of the gene in the virus in terms of nucleotide composition and amino acid sequence. The NrdJm enzyme is a monomeric B12-dependent RNR with nucleoside triphosphate specificity. It exhibits a temperature optimum at 60–70 °C, which is in the range of the growth optimum of Thermus spp. Experiments in combination with the Thermus thermophilus thioredoxin system show that the enzyme is able to retrieve electrons from the host NADPH pool via host thioredoxin and thioredoxin reductases. This is different from other characterized viral RNRs such as T4 phage RNR, where a viral thioredoxin is present. We hence show that the monomeric class II RNR, present in Thermus viruses, was likely transferred from an organism phylogenetically distant from the one they were isolated from, and adapted to the new host in genetic signature and amino acids sequence.
Collapse
Affiliation(s)
- Christoph Loderer
- Institute for Microbiology, Technische Universität Dresden, Dresden, Saxony, Germany
| | - Karin Holmfeldt
- Centre for Ecology and Evolution in Microbial model Systems-EEMiS, Linnaeus University, Kalmar, Sweden
| | - Daniel Lundin
- Centre for Ecology and Evolution in Microbial model Systems-EEMiS, Linnaeus University, Kalmar, Sweden.,Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| |
Collapse
|
12
|
Buey RM, Schmitz RA, Buchanan BB, Balsera M. Crystal Structure of the Apo-Form of NADPH-Dependent Thioredoxin Reductase from a Methane-Producing Archaeon. Antioxidants (Basel) 2018; 7:E166. [PMID: 30453601 PMCID: PMC6262447 DOI: 10.3390/antiox7110166] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Revised: 11/12/2018] [Accepted: 11/14/2018] [Indexed: 12/20/2022] Open
Abstract
The redox regulation of proteins via reversible dithiol/disulfide exchange reactions involves the thioredoxin system, which is composed of a reductant, a thioredoxin reductase (TR), and thioredoxin (Trx). In the pyridine nucleotide-dependent Trx reduction pathway, reducing equivalents, typically from reduced nicotinamide adenine dinucleotide phosphate (NADPH), are transferred from NADPH-TR (NTR) to Trx and, in turn, to target proteins, thus resulting in the reversible modification of the structural and functional properties of the targets. NTR enzymes contain three functional sites: an NADPH binding pocket, a non-covalently bound flavin cofactor, and a redox-active disulfide in the form of CxxC. With the aim of increasing our knowledge of the thioredoxin system in archaea, we here report the high-resolution crystal structure of NTR from the methane-generating organism Methanosarcina mazei strain Gö1 (MmNTR) at 2.6 Å resolution. Based on the crystals presently described, MmNTR assumes an overall fold that is nearly identical to the archetypal fold of authentic NTRs; however, surprisingly, we observed no electron density for flavin adenine dinucleotide (FAD) despite the well-defined and conserved FAD-binding cavity in the folded module. Remarkably, the dimers of the apo-protein within the crystal were different from those observed by small angle X-ray scattering (SAXS) for the holo-protein, suggesting that the binding of the flavin cofactor does not require major protein structural rearrangements. Rather, binding results in the stabilization of essential parts of the structure, such as those involved in dimer stabilization. Altogether, this structure represents the example of an apo-form of an NTR that yields important insight into the effects of the cofactor on protein folding.
Collapse
Affiliation(s)
- Rubén M Buey
- Metabolic Engineering Group. Dpto. Microbiología y Genética. Universidad de Salamanca, 37007 Salamanca, Spain.
| | - Ruth A Schmitz
- Institut für Allgemeine Mikrobiologie, Christian-Albrechts-Universität Kiel, 24118 Kiel, Germany.
| | - Bob B Buchanan
- Department of Plant & Microbial Biology, University of California, 94720 Berkeley CA, USA.
| | - Monica Balsera
- Instituto de Recursos Naturales y Agrobiología de Salamanca (IRNASA-CSIC), 37008 Salamanca, Spain.
| |
Collapse
|
13
|
Indoleacetate decarboxylase is a glycyl radical enzyme catalysing the formation of malodorant skatole. Nat Commun 2018; 9:4224. [PMID: 30310076 PMCID: PMC6181972 DOI: 10.1038/s41467-018-06627-x] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 09/07/2018] [Indexed: 12/30/2022] Open
Abstract
Skatole is a malodorous compound that contributes to the characteristic smell of animal faeces. Although skatole has long been known to originate from bacterial tryptophan fermentation, the enzyme catalysing its formation has so far remained elusive. Here we report the use of comparative genomics for the discovery of indoleacetate decarboxylase, an O2-sensitive glycyl radical enzyme catalysing the decarboxylation of indoleacetate to form skatole as the terminal step of tryptophan fermentation in certain anaerobic bacteria. We describe its biochemical characterization and compare it to other glycyl radical decarboxylases. Indoleacetate decarboxylase may serve as a genetic marker for the identification of skatole-producing environmental and human-associated bacteria, with impacts on human health and the livestock industry. Skatole is a bacterial metabolite responsible for boar taint and the objectionable smell of manure. Here, the authors elucidate the final step of skatole biosynthesis, describing the discovery and biochemical characterization of the enzyme catalysing the conversion of indoleacetate into skatole.
Collapse
|
14
|
Prakash D, Walters KA, Martinie RJ, McCarver AC, Kumar AK, Lessner DJ, Krebs C, Golbeck JH, Ferry JG. Toward a mechanistic and physiological understanding of a ferredoxin:disulfide reductase from the domains Archaea and Bacteria. J Biol Chem 2018; 293:9198-9209. [PMID: 29720404 DOI: 10.1074/jbc.ra118.002473] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Revised: 04/24/2018] [Indexed: 11/06/2022] Open
Abstract
Disulfide reductases reduce other proteins and are critically important for cellular redox signaling and homeostasis. Methanosarcina acetivorans is a methane-producing microbe from the domain Archaea that produces a ferredoxin:disulfide reductase (FDR) for which the crystal structure has been reported, yet its biochemical mechanism and physiological substrates are unknown. FDR and the extensively characterized plant-type ferredoxin:thioredoxin reductase (FTR) belong to a distinct class of disulfide reductases that contain a unique active-site [4Fe-4S] cluster. The results reported here support a mechanism for FDR similar to that reported for FTR with notable exceptions. Unlike FTR, FDR contains a rubredoxin [1Fe-0S] center postulated to mediate electron transfer from ferredoxin to the active-site [4Fe-4S] cluster. UV-visible, EPR, and Mössbauer spectroscopic data indicated that two-electron reduction of the active-site disulfide in FDR involves a one-electron-reduced [4Fe-4S]1+ intermediate previously hypothesized for FTR. Our results support a role for an active-site tyrosine in FDR that occupies the equivalent position of an essential histidine in the active site of FTR. Of note, one of seven Trxs encoded in the genome (Trx5) and methanoredoxin, a glutaredoxin-like enzyme from M. acetivorans, were reduced by FDR, advancing the physiological understanding of FDR's role in the redox metabolism of methanoarchaea. Finally, bioinformatics analyses show that FDR homologs are widespread in diverse microbes from the domain Bacteria.
Collapse
Affiliation(s)
- Divya Prakash
- From the Departments of Biochemistry and Molecular Biology and
| | - Karim A Walters
- From the Departments of Biochemistry and Molecular Biology and
| | - Ryan J Martinie
- Chemistry, Pennsylvania State University, University Park, Pennsylvania 16802 and
| | - Addison C McCarver
- the Department of Biological Sciences, University of Arkansas, Fayetteville, Arkansas 72701
| | - Adepu K Kumar
- From the Departments of Biochemistry and Molecular Biology and
| | - Daniel J Lessner
- the Department of Biological Sciences, University of Arkansas, Fayetteville, Arkansas 72701
| | - Carsten Krebs
- From the Departments of Biochemistry and Molecular Biology and.,Chemistry, Pennsylvania State University, University Park, Pennsylvania 16802 and
| | - John H Golbeck
- From the Departments of Biochemistry and Molecular Biology and.,Chemistry, Pennsylvania State University, University Park, Pennsylvania 16802 and
| | - James G Ferry
- From the Departments of Biochemistry and Molecular Biology and
| |
Collapse
|
15
|
Loderer C, Jonna VR, Crona M, Rozman Grinberg I, Sahlin M, Hofer A, Lundin D, Sjöberg BM. A unique cysteine-rich zinc finger domain present in a majority of class II ribonucleotide reductases mediates catalytic turnover. J Biol Chem 2017; 292:19044-19054. [PMID: 28972190 PMCID: PMC5704485 DOI: 10.1074/jbc.m117.806331] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Revised: 09/28/2017] [Indexed: 12/04/2022] Open
Abstract
Ribonucleotide reductases (RNRs) catalyze the reduction of ribonucleotides to the corresponding deoxyribonucleotides, used in DNA synthesis and repair. Two different mechanisms help deliver the required electrons to the RNR active site. Formate can be used as reductant directly in the active site, or glutaredoxins or thioredoxins reduce a C-terminal cysteine pair, which then delivers the electrons to the active site. Here, we characterized a novel cysteine-rich C-terminal domain (CRD), which is present in most class II RNRs found in microbes. The NrdJd-type RNR from the bacterium Stackebrandtia nassauensis was used as a model enzyme. We show that the CRD is involved in both higher oligomeric state formation and electron transfer to the active site. The CRD-dependent formation of high oligomers, such as tetramers and hexamers, was induced by addition of dATP or dGTP, but not of dTTP or dCTP. The electron transfer was mediated by an array of six cysteine residues at the very C-terminal end, which also coordinated a zinc atom. The electron transfer can also occur between subunits, depending on the enzyme's oligomeric state. An investigation of the native reductant of the system revealed no interaction with glutaredoxins or thioredoxins, indicating that this class II RNR uses a different electron source. Our results indicate that the CRD has a crucial role in catalytic turnover and a potentially new terminal reduction mechanism and suggest that the CRD is important for the activities of many class II RNRs.
Collapse
Affiliation(s)
- Christoph Loderer
- From the Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden and
| | | | - Mikael Crona
- From the Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden and
| | - Inna Rozman Grinberg
- From the Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden and
| | - Margareta Sahlin
- From the Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden and
| | - Anders Hofer
- the Department of Medical Biochemistry, Umeå University, SE-901 87 Umeå, Sweden
| | - Daniel Lundin
- From the Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden and
| | - Britt-Marie Sjöberg
- From the Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden and
| |
Collapse
|
16
|
Levin BJ, Huang YY, Peck SC, Wei Y, Martínez-Del Campo A, Marks JA, Franzosa EA, Huttenhower C, Balskus EP. A prominent glycyl radical enzyme in human gut microbiomes metabolizes trans-4-hydroxy-l-proline. Science 2017; 355:355/6325/eaai8386. [PMID: 28183913 DOI: 10.1126/science.aai8386] [Citation(s) in RCA: 102] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 01/04/2017] [Indexed: 12/14/2022]
Abstract
The human microbiome encodes vast numbers of uncharacterized enzymes, limiting our functional understanding of this community and its effects on host health and disease. By incorporating information about enzymatic chemistry into quantitative metagenomics, we determined the abundance and distribution of individual members of the glycyl radical enzyme superfamily among the microbiomes of healthy humans. We identified many uncharacterized family members, including a universally distributed enzyme that enables commensal gut microbes and human pathogens to dehydrate trans-4-hydroxy-l-proline, the product of the most abundant human posttranslational modification. This "chemically guided functional profiling" workflow can therefore use ecological context to facilitate the discovery of enzymes in microbial communities.
Collapse
Affiliation(s)
- B J Levin
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA
| | - Y Y Huang
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA
| | - S C Peck
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA
| | - Y Wei
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - A Martínez-Del Campo
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA
| | - J A Marks
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA
| | - E A Franzosa
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA.,Broad Institute, Cambridge, MA 02139, USA
| | - C Huttenhower
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA.,Broad Institute, Cambridge, MA 02139, USA
| | - E P Balskus
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA. .,Broad Institute, Cambridge, MA 02139, USA
| |
Collapse
|
17
|
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
|
18
|
McCarver AC, Lessner FH, Soroeta JM, Lessner DJ. Methanosarcina acetivorans utilizes a single NADPH-dependent thioredoxin system and contains additional thioredoxin homologues with distinct functions. MICROBIOLOGY-SGM 2017; 163:62-74. [PMID: 27902413 DOI: 10.1099/mic.0.000406] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The thioredoxin system plays a central role in the intracellular redox maintenance in the majority of cells. The canonical system consists of an NADPH-dependent thioredoxin reductase (TrxR) and thioredoxin (Trx), a disulfide reductase. Although Trx is encoded in almost all sequenced genomes of methanogens, its incorporation into their unique physiology is not well understood. Methanosarcina acetivorans contains a single TrxR (MaTrxR) and seven Trx (MaTrx1-MaTrx7) homologues. We previously showed that MaTrxR and at least MaTrx7 compose a functional NADPH-dependent thioredoxin system. Here, we report the characterization of all seven recombinant MaTrxs. MaTrx1, MaTrx3, MaTrx4 and MaTrx5 lack appreciable disulfide reductase activity, unlike previously characterized MaTrx2, MaTrx6 and MaTrx7. Enzyme assays demonstrated that, of the MaTrxs, only the reduction of disulfide-containing MaTrx7 is linked to the oxidation of reduced coenzymes. NADPH is shown to be supplied to the MaTrxR-MaTrx7 system through the oxidation of the primary methanogen electron carriers F420H2 and ferredoxin, indicating that it serves as a primary intracellular reducing system in M. acetivorans. Bioinformatic analyses also indicate that the majority of methanogens likely utilize an NADPH-dependent thioredoxin system. The remaining MaTrxs may have specialized functions. MaTrx1 and MaTrx3 exhibited thiol oxidase activity. MaTrx3 and MaTrx6 are targeted to the membrane of M. acetivorans and likely function in the formation and the reduction of disulfides in membrane and/or extracellular proteins, respectively. This work provides insight into the incorporation of Trx into the metabolism of methanogens, and this reveals that methanogens contain Trx homologues with alternative properties and activities.
Collapse
Affiliation(s)
- Addison C McCarver
- Department of Biological Sciences, University of Arkansas-Fayetteville, Fayetteville, AR 72701, USA
| | - Faith H Lessner
- Department of Biological Sciences, University of Arkansas-Fayetteville, Fayetteville, AR 72701, USA
| | - Jose M Soroeta
- Department of Biological Sciences, University of Arkansas-Fayetteville, Fayetteville, AR 72701, USA
| | - Daniel J Lessner
- Department of Biological Sciences, University of Arkansas-Fayetteville, Fayetteville, AR 72701, USA
| |
Collapse
|