1
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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.
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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
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2
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Pugazhendhi AS, Neal CJ, Ta KM, Molinari M, Kumar U, Wei F, Kolanthai E, Ady A, Drake C, Hughes M, Yooseph S, Seal S, Coathup MJ. A neoteric antibacterial ceria-silver nanozyme for abiotic surfaces. Biomaterials 2024; 307:122527. [PMID: 38518591 DOI: 10.1016/j.biomaterials.2024.122527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 03/01/2024] [Accepted: 03/08/2024] [Indexed: 03/24/2024]
Abstract
Community-associated and hospital-acquired infections caused by bacteria continue to yield major global challenges to human health. Bacterial contamination on abiotic surfaces is largely spread via high-touch surfaces and contemporary standard disinfection practices show limited efficacy, resulting in unsatisfactory therapeutic outcomes. New strategies that offer non-specific and broad protection are urgently needed. Herein, we report our novel ceria-silver nanozyme engineered at a molar ratio of 5:1 and with a higher trivalent (Ce3+) surface fraction. Our results reveal potent levels of surface catalytic activity on both wet and dry surfaces, with rapid, and complete eradication of Pseudomonas aeruginosa, Staphylococcus aureus, and methicillin resistant S. aureus, in both planktonic and biofilm form. Preferential electrostatic adherence of anionic bacteria to the cationic nanozyme surface leads to a catastrophic loss in both aerobic and anaerobic respiration, DNA damage, osmodysregulation, and finally, programmed bacterial lysis. Our data reveal several unique mechanistic avenues of synergistic ceria-Ag efficacy. Ag potentially increases the presence of Ce3+ sites at the ceria-Ag interface, thereby facilitating the formation of harmful H2O2, followed by likely permeation across the cell wall. Further, a weakened Ag-induced Ce-O bond may drive electron transfer from the Ec band to O2, thereby further facilitating the selective reduction of O2 toward H2O2 formation. Ag destabilizes the surface adsorption of molecular H2O2, potentially leading to higher concentrations of free H2O2 adjacent to bacteria. To this end, our results show that H2O2 and/or NO/NO2-/NO3- are the key liberators of antibacterial activity, with a limited immediate role being offered by nanozyme-induced ROS including O2•- and OH•, and likely other light-activated radicals. A mini-pilot proof-of-concept study performed in a pediatric dental clinic setting confirms residual, and continual nanozyme antibacterial efficacy over a 28-day period. These findings open a new approach to alleviate infections caused by bacteria for use on high-touch hard surfaces.
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Affiliation(s)
- Abinaya Sindu Pugazhendhi
- Biionix Cluster, College of Medicine, University of Central Florida, Orlando, FL, 32827, United States
| | - Craig J Neal
- Advanced Materials Processing and Analysis Centre, Nanoscience Technology Center (NSTC), University of Central Florida, Orlando, FL, 32826, United States
| | - Khoa Minh Ta
- Department of Chemical Sciences, School of Applied Sciences, University of Huddersfield, Huddersfield, HD1 3DH, United Kingdom
| | - Marco Molinari
- Department of Chemical Sciences, School of Applied Sciences, University of Huddersfield, Huddersfield, HD1 3DH, United Kingdom.
| | - Udit Kumar
- Advanced Materials Processing and Analysis Centre, Nanoscience Technology Center (NSTC), University of Central Florida, Orlando, FL, 32826, United States
| | - Fei Wei
- Biionix Cluster, College of Medicine, University of Central Florida, Orlando, FL, 32827, United States
| | - Elayaraja Kolanthai
- Advanced Materials Processing and Analysis Centre, Nanoscience Technology Center (NSTC), University of Central Florida, Orlando, FL, 32826, United States
| | - Andrew Ady
- Biionix Cluster, College of Medicine, University of Central Florida, Orlando, FL, 32827, United States
| | - Christina Drake
- Kismet Technologies, 7101 TPC Drive, Suite 130, Orlando, FL, 32822, United States
| | - Megan Hughes
- University of Cardiff, Cardiff, CF10 3AT, Wales, United Kingdom
| | - Shibu Yooseph
- Kravis Department of Integrated Sciences, Claremont McKenna College, Claremont, CA 91711, United States
| | - Sudipta Seal
- Biionix Cluster, College of Medicine, University of Central Florida, Orlando, FL, 32827, United States; Advanced Materials Processing and Analysis Centre, Nanoscience Technology Center (NSTC), University of Central Florida, Orlando, FL, 32826, United States
| | - Melanie J Coathup
- Biionix Cluster, College of Medicine, University of Central Florida, Orlando, FL, 32827, United States.
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3
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Kammel M, Erdmann C, Sawers RG. The formate-hydrogen axis and its impact on the physiology of enterobacterial fermentation. Adv Microb Physiol 2024; 84:51-82. [PMID: 38821634 DOI: 10.1016/bs.ampbs.2024.02.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2024]
Abstract
Formic acid (HCOOH) and dihydrogen (H2) are characteristic products of enterobacterial mixed-acid fermentation, with H2 generation increasing in conjunction with a decrease in extracellular pH. Formate and acetyl-CoA are generated by radical-based and coenzyme A-dependent cleavage of pyruvate catalysed by pyruvate formate-lyase (PflB). Formate is also the source of H2, which is generated along with carbon dioxide through the action of the membrane-associated, cytoplasmically-oriented formate hydrogenlyase (FHL-1) complex. Synthesis of the FHL-1 complex is completely dependent on the cytoplasmic accumulation of formate. Consequently, formate determines its own disproportionation into H2 and CO2 by the FHL-1 complex. Cytoplasmic formate levels are controlled by FocA, a pentameric channel that translocates formic acid/formate bidirectionally between the cytoplasm and periplasm. Each protomer of FocA has a narrow hydrophobic pore through which neutral formic acid can pass. Two conserved amino acid residues, a histidine and a threonine, at the center of the pore control directionality of translocation. The histidine residue is essential for pH-dependent influx of formic acid. Studies with the formate analogue hypophosphite and amino acid variants of FocA suggest that the mechanisms of formic acid efflux and influx differ. Indeed, current data suggest, depending on extracellular formate levels, two separate uptake mechanisms exist, both likely contributing to maintain pH homeostasis. Bidirectional formate/formic acid translocation is dependent on PflB and influx requires an active FHL-1 complex. This review describes the coupling of formate and H2 production in enterobacteria.
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Affiliation(s)
- Michelle Kammel
- Institute of Microbiology, Martin Luther University Halle-Wittenberg, Halle, Saale, Germany
| | - Christopher Erdmann
- Institute of Microbiology, Martin Luther University Halle-Wittenberg, Halle, Saale, Germany
| | - R Gary Sawers
- Institute of Microbiology, Martin Luther University Halle-Wittenberg, Halle, Saale, Germany.
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4
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Walls WG, Vagstad A, Delridge T, Piel J, Broderick WE, Broderick JB. Direct Detection of the α-Carbon Radical Intermediate Formed by OspD: Mechanistic Insights into Radical S-Adenosyl-l-methionine Peptide Epimerization. J Am Chem Soc 2024; 146:5550-5559. [PMID: 38364824 PMCID: PMC11302384 DOI: 10.1021/jacs.3c13829] [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] [Indexed: 02/18/2024]
Abstract
OspD is a radical S-adenosyl-l-methionine (SAM) peptide epimerase that converts an isoleucine (Ile) and valine (Val) of the OspA substrate to d-amino acids during biosynthesis of the ribosomally synthesized and post-translationally modified peptide (RiPP) natural product landornamide A. OspD is proposed to carry out this reaction via α-carbon (Cα) H-atom abstraction to form a peptidyl Cα radical that is stereospecifically quenched by hydrogen atom transfer (HAT) from a conserved cysteine (Cys). Here we use site-directed mutagenesis, freeze-quench trapping, isotopic labeling, and electron paramagnetic resonance (EPR) spectroscopy to provide new insights into the OspD catalytic mechanism including the direct observation of the substrate peptide Cα radical intermediate. The putative quenching Cys334 was changed to serine to generate an OspD C334S variant impaired in HAT quenching. The reaction of reduced OspD C334S with SAM and OspA freeze-quenched at 15 s exhibits a doublet EPR signal characteristic of a Cα radical coupled to a single β-H. Using isotopologues of OspA deuterated at either Ile or Val, or both Ile and Val, reveals that the initial Cα radical intermediate forms exclusively on the Ile of OspA. Time-dependent freeze quench coupled with EPR spectroscopy provided evidence for loss of the Ile Cα radical concomitant with gain of a Val Cα radical, directly demonstrating the N-to-C directionality of epimerization by OspD. These results provide direct evidence for the aforementioned OspD-catalyzed peptide epimerization mechanism via a central Cα radical intermediate during RiPP maturation of OspA, a mechanism that may extend to other proteusin peptide epimerases.
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Affiliation(s)
- William G. Walls
- Department of Chemistry & Biochemistry, Montana State University, Bozeman, MT 59717, United States
| | - Anna Vagstad
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Vladimir-Prelog-Weg 4, Zürich 8093, Switzerland
| | - Tyler Delridge
- Department of Chemistry & Biochemistry, Montana State University, Bozeman, MT 59717, United States
| | - Jörn Piel
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Vladimir-Prelog-Weg 4, Zürich 8093, Switzerland
| | - William E. Broderick
- Department of Chemistry & Biochemistry, Montana State University, Bozeman, MT 59717, United States
| | - Joan B. Broderick
- Department of Chemistry & Biochemistry, Montana State University, Bozeman, MT 59717, United States
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5
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Lundahl MN, Yang H, Broderick WE, Hoffman BM, Broderick JB. Pyruvate formate-lyase activating enzyme: The catalytically active 5'-deoxyadenosyl radical caught in the act of H-atom abstraction. Proc Natl Acad Sci U S A 2023; 120:e2314696120. [PMID: 37956301 PMCID: PMC10665898 DOI: 10.1073/pnas.2314696120] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 10/03/2023] [Indexed: 11/15/2023] Open
Abstract
Enzymes of the radical S-adenosyl-l-methionine (radical SAM, RS) superfamily, the largest in nature, catalyze remarkably diverse reactions initiated by H-atom abstraction. Glycyl radical enzyme activating enzymes (GRE-AEs) are a growing class of RS enzymes that generate the catalytically essential glycyl radical of GREs, which in turn catalyze essential reactions in anaerobic metabolism. Here, we probe the reaction of the GRE-AE pyruvate formate-lyase activating enzyme (PFL-AE) with the peptide substrate RVSG734YAV, which mimics the site of glycyl radical formation on the native substrate, pyruvate formate-lyase. Time-resolved freeze-quench electron paramagnetic resonance spectroscopy shows that at short mixing times reduced PFL-AE + SAM reacts with RVSG734YAV to form the central organometallic intermediate, Ω, in which the adenosyl 5'C is covalently bound to the unique iron of the [4Fe-4S] cluster. Freeze-trapping the reaction at longer times reveals the formation of the peptide G734• glycyl radical product. Of central importance, freeze-quenching at intermediate times reveals that the conversion of Ω to peptide glycyl radical is not concerted. Instead, homolysis of the Ω Fe-C5' bond generates the nominally "free" 5'-dAdo• radical, which is captured here by freeze-trapping. During cryoannealing at 77 K, the 5'-dAdo• directly abstracts an H-atom from the peptide to generate the G734• peptide radical trapped in the PFL-AE active site. These observations reveal the 5'-dAdo• radical to be a well-defined intermediate, caught in the act of substrate H-atom abstraction, providing new insights into the mechanistic steps of radical initiation by RS enzymes.
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Affiliation(s)
- Maike N. Lundahl
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT59717
| | - Hao Yang
- Department of Chemistry, Northwestern University, Evanston, IL60208
| | - William E. Broderick
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT59717
| | - Brian M. Hoffman
- Department of Chemistry, Northwestern University, Evanston, IL60208
| | - Joan B. Broderick
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT59717
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6
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Cáceres JC, Dolmatch A, Greene BL. The Mechanism of Inhibition of Pyruvate Formate Lyase by Methacrylate. J Am Chem Soc 2023; 145:22504-22515. [PMID: 37797332 PMCID: PMC10591478 DOI: 10.1021/jacs.3c07256] [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: 07/08/2023] [Indexed: 10/07/2023]
Abstract
Pyruvate Formate Lyase (PFL) catalyzes acetyl transfer from pyruvate to coenzyme a by a mechanism involving multiple amino acid radicals. A post-translationally installed glycyl radical (G734· in Escherichia coli) is essential for enzyme activity and two cysteines (C418 and C419) are proposed to form thiyl radicals during turnover, yet their unique roles in catalysis have not been directly demonstrated with both structural and electronic resolution. Methacrylate is an isostructural analog of pyruvate and an informative irreversible inhibitor of pfl. Here we demonstrate the mechanism of inhibition of pfl by methacrylate. Treatment of activated pfl with methacrylate results in the conversion of the G734· to a new radical species, concomitant with enzyme inhibition, centered at g = 2.0033. Spectral simulations, reactions with methacrylate isotopologues, and Density Functional Theory (DFT) calculations support our assignment of the radical to a C2 tertiary methacryl radical. The reaction is specific for C418, as evidenced by mass spectrometry. The methacryl radical decays over time, reforming G734·, and the decay exhibits a H/D solvent isotope effect of 3.4, consistent with H-atom transfer from an ionizable donor, presumably the C419 sulfhydryl group. Acrylate also inhibits PFL irreversibly, and alkylates C418, but we did not observe an acryl secondary radical in H2O or in D2O within 10 s, consistent with our DFT calculations and the expected reactivity of a secondary versus tertiary carbon-centered radical. Together, the results support unique roles of the two active site cysteines of PFL and a C419 S-H bond dissociation energy between that of a secondary and tertiary C-H bond.
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Affiliation(s)
- Juan Carlos Cáceres
- Biomolecular
Science and Engineering Program, University
of California, Santa
Barbara, California 93106, United States
| | - August Dolmatch
- Department
of Chemistry and Biochemistry, University
of California, Santa Barbara, California 93106, United States
| | - Brandon L. Greene
- Biomolecular
Science and Engineering Program, University
of California, Santa
Barbara, California 93106, United States
- Department
of Chemistry and Biochemistry, University
of California, Santa Barbara, California 93106, United States
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7
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Abstract
Radical S-adenosylmethionine (SAM) enzymes use a site-differentiated [4Fe-4S] cluster and SAM to initiate radical reactions through liberation of the 5'-deoxyadenosyl (5'-dAdo•) radical. They form the largest enzyme superfamily, with more than 700,000 unique sequences currently, and their numbers continue to grow as a result of ongoing bioinformatics efforts. The range of extremely diverse, highly regio- and stereo-specific reactions known to be catalyzed by radical SAM superfamily members is remarkable. The common mechanism of radical initiation in the radical SAM superfamily is the focus of this review. Most surprising is the presence of an organometallic intermediate, Ω, exhibiting an Fe-C5'-adenosyl bond. Regioselective reductive cleavage of the SAM S-C5' bond produces 5'-dAdo• to form Ω, with the regioselectivity originating in the Jahn-Teller effect. Ω liberates the free 5'-dAdo• as the catalytically active intermediate through homolysis of the Fe-C5' bond, in analogy to Co-C5' bond homolysis in B12, which was once viewed as biology's choice of radical generator.
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Affiliation(s)
- Brian M Hoffman
- Department of Chemistry, Northwestern University, Evanston, Illinois, USA
| | - William E Broderick
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA;
| | - Joan B Broderick
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA;
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8
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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.
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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
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9
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Harrison MA, Farthing RJ, Allen N, Ahern LM, Birchall K, Bond M, Kaur H, Wren BW, Bergeron JRC, Dawson LF. Identification of novel p-cresol inhibitors that reduce Clostridioides difficile's ability to compete with species of the gut microbiome. Sci Rep 2023; 13:9492. [PMID: 37303029 PMCID: PMC10258198 DOI: 10.1038/s41598-023-32656-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 03/30/2023] [Indexed: 06/13/2023] Open
Abstract
Treatment of Clostridioides difficile infection (CDI) is expensive and complex, with a high proportion of patients suffering infection relapse (20-35%), and some having multiple relapses. A healthy, unperturbed gut microbiome provides colonisation resistance against CDI through competition for nutrients and space. However, antibiotic consumption can disturb the gut microbiota (dysbiosis) resulting in the loss of colonisation resistance allowing C. difficile to colonise and establish infection. A unique feature of C. difficile is the production of high concentrations of the antimicrobial compound para-cresol, which provides the bacterium with a competitive advantage over other bacteria found in the gut. p-cresol is produced by the conversion of para-Hydroxyphenylacetic acid (p-HPA) by the HpdBCA enzyme complex. In this study, we have identified several promising inhibitors of HpdBCA decarboxylase, which reduce p-cresol production and render C. difficile less able to compete with a gut dwelling Escherichia coli strain. We demonstrate that the lead compound, 4-Hydroxyphenylacetonitrile, reduced p-cresol production by 99.0 ± 0.4%, whereas 4-Hydroxyphenylacetamide, a previously identified inhibitor of HpdBCA decarboxylase, only reduced p-cresol production by 54.9 ± 13.5%. To interpret efficacy of these first-generation inhibitors, we undertook molecular docking studies that predict the binding mode for these compounds. Notably, the predicted binding energy correlated well with the experimentally determined level of inhibition, providing a molecular basis for the differences in efficacy between the compounds. This study has identified promising p-cresol production inhibitors whose development could lead to beneficial therapeutics that help to restore colonisation resistance and therefore reduce the likelihood of CDI relapse.
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Affiliation(s)
- Mark A Harrison
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | - Rebecca J Farthing
- Randall Centre for Cell and Molecular Biophysics, King's College London, London, WC2R 2LS, UK
| | - Nyasha Allen
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | - Lucy M Ahern
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | | | - Michael Bond
- LifeArc, Lynton House, 7-12 Tavistock Square, London, WC1H 9LT, UK
| | - Harparkash Kaur
- Department of Clinical Research, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | - Brendan W Wren
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | - Julien R C Bergeron
- Randall Centre for Cell and Molecular Biophysics, King's College London, London, WC2R 2LS, UK
| | - Lisa F Dawson
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK.
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10
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Moody JD, Hill S, Lundahl MN, Saxton AJ, Galambas A, Broderick WE, Lawrence CM, Broderick JB. Computational engineering of previously crystallized pyruvate formate-lyase activating enzyme reveals insights into SAM binding and reductive cleavage. J Biol Chem 2023; 299:104791. [PMID: 37156396 PMCID: PMC10267522 DOI: 10.1016/j.jbc.2023.104791] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 04/21/2023] [Accepted: 04/23/2023] [Indexed: 05/10/2023] Open
Abstract
Radical S-adenosyl-l-methionine (SAM) enzymes are ubiquitous in nature and carry out a broad variety of difficult chemical transformations initiated by hydrogen atom abstraction. Although numerous radical SAM (RS) enzymes have been structurally characterized, many prove recalcitrant to crystallization needed for atomic-level structure determination using X-ray crystallography, and even those that have been crystallized for an initial study can be difficult to recrystallize for further structural work. We present here a method for computationally engineering previously observed crystallographic contacts and employ it to obtain more reproducible crystallization of the RS enzyme pyruvate formate-lyase activating enzyme (PFL-AE). We show that the computationally engineered variant binds a typical RS [4Fe-4S]2+/+ cluster that binds SAM, with electron paramagnetic resonance properties indistinguishable from the native PFL-AE. The variant also retains the typical PFL-AE catalytic activity, as evidenced by the characteristic glycyl radical electron paramagnetic resonance signal observed upon incubation of the PFL-AE variant with reducing agent, SAM, and PFL. The PFL-AE variant was also crystallized in the [4Fe-4S]2+ state with SAM bound, providing a new high-resolution structure of the SAM complex in the absence of substrate. Finally, by incubating such a crystal in a solution of sodium dithionite, the reductive cleavage of SAM is triggered, providing us with a structure in which the SAM cleavage products 5'-deoxyadenosine and methionine are bound in the active site. We propose that the methods described herein may be useful in the structural characterization of other difficult-to-resolve proteins.
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Affiliation(s)
- James D Moody
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah, USA; Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA
| | - Sarah Hill
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA
| | - Maike N Lundahl
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA
| | - Aubrianna J Saxton
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah, USA
| | - Amanda Galambas
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA
| | - William E Broderick
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA
| | - C Martin Lawrence
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA
| | - Joan B Broderick
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA.
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11
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Broderick JB, Broderick WE, Hoffman BM. Radical SAM enzymes: Nature's choice for radical reactions. FEBS Lett 2023; 597:92-101. [PMID: 36251330 PMCID: PMC9894703 DOI: 10.1002/1873-3468.14519] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 10/05/2022] [Indexed: 02/04/2023]
Abstract
Enzymes that use a [4Fe-4S]1+ cluster plus S-adenosyl-l-methionine (SAM) to initiate radical reactions (radical SAM) form the largest enzyme superfamily, with over half a million members across the tree of life. This review summarizes recent work revealing the radical SAM reaction pathway, which ultimately liberates the 5'-deoxyadenosyl (5'-dAdo•) radical to perform extremely diverse, highly regio- and stereo-specific, transformations. Most surprising was the discovery of an organometallic intermediate Ω exhibiting an Fe-C5'-adenosyl bond. Ω liberates 5'-dAdo• through homolysis of the Fe-C5' bond, in analogy to Co-C5' bond homolysis in B12 , previously viewed as biology's paradigmatic radical generator. The 5'-dAdo• has been trapped and characterized in radical SAM enzymes via a recently discovered photoreactivity of the [4Fe-4S]+ /SAM complex, and has been confirmed as a catalytically active intermediate in enzyme catalysis. The regioselective SAM S-C bond cleavage to produce 5'-dAdo• originates in the Jahn-Teller effect. The simplicity of SAM as a radical precursor, and the exquisite control of 5'-dAdo• reactivity in radical SAM enzymes, may be why radical SAM enzymes pervade the tree of life, while B12 enzymes are only a few.
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Affiliation(s)
- Joan B. Broderick
- Department of Chemistry & Biochemistry, 103 CBB, Montana State University, Bozeman, MT 59717
| | - William E. Broderick
- Department of Chemistry & Biochemistry, 103 CBB, Montana State University, Bozeman, MT 59717
| | - Brian M. Hoffman
- Department of Chemistry, 2145 Sheridan Rd, Northwestern University, Evanston, IL. 60208
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12
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Booker SJ, Lloyd CT. Twenty Years of Radical SAM! The Genesis of the Superfamily. ACS BIO & MED CHEM AU 2022; 2:538-547. [PMID: 37101427 PMCID: PMC10114671 DOI: 10.1021/acsbiomedchemau.2c00078] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Indexed: 12/10/2022]
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13
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Hanževački M, Croft AK, Jäger CM. Activation of Glycyl Radical Enzymes─Multiscale Modeling Insights into Catalysis and Radical Control in a Pyruvate Formate-Lyase-Activating Enzyme. J Chem Inf Model 2022; 62:3401-3414. [PMID: 35771966 PMCID: PMC9326890 DOI: 10.1021/acs.jcim.2c00362] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Pyruvate formate-lyase (PFL) is a glycyl radical enzyme (GRE) playing a pivotal role in the metabolism of strict and facultative anaerobes. Its activation is carried out by a PFL-activating enzyme, a member of the radical S-adenosylmethionine (rSAM) superfamily of metalloenzymes, which introduces a glycyl radical into the Gly radical domain of PFL. The activation mechanism is still not fully understood and is structurally based on a complex with a short model peptide of PFL. Here, we present extensive molecular dynamics simulations in combination with quantum mechanics/molecular mechanics (QM/MM)-based kinetic and thermodynamic reaction evaluations of a more complete activation model comprising the 49 amino acid long C-terminus region of PFL. We reveal the benefits and pitfalls of the current activation model, providing evidence that the bound peptide conformation does not resemble the bound protein-protein complex conformation with PFL, with implications for the activation process. Substitution of the central glycine with (S)- and (R)-alanine showed excellent binding of (R)-alanine over unstable binding of (S)-alanine. Radical stabilization calculations indicate that a higher radical stability of the glycyl radical might not be the sole origin of the evolutionary development of GREs. QM/MM-derived radical formation kinetics further demonstrate feasible activation barriers for both peptide and C-terminus activation, demonstrating why the crystalized model peptide system is an excellent inhibitory system for natural activation. This new evidence supports the theory that GREs converged on glycyl radical formation due to the better conformational accessibility of the glycine radical loop, rather than the highest radical stability of the formed peptide radicals.
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Affiliation(s)
- Marko Hanževački
- Department of Chemical and Environmental Engineering, University of Nottingham, Nottingham NG7 2RD, U.K
| | - Anna K Croft
- Department of Chemical and Environmental Engineering, University of Nottingham, Nottingham NG7 2RD, U.K
| | - Christof M Jäger
- Department of Chemical and Environmental Engineering, University of Nottingham, Nottingham NG7 2RD, U.K
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14
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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: 2] [Impact Index Per Article: 1.0] [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.
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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
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15
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The Autonomous Glycyl Radical Protein GrcA Restores Activity to Inactive Full-Length Pyruvate Formate-Lyase In Vivo. J Bacteriol 2022; 204:e0007022. [PMID: 35377165 DOI: 10.1128/jb.00070-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
During glucose fermentation, Escherichia coli and many other microorganisms employ the glycyl radical enzyme (GRE) pyruvate formate-lyase (PflB) to catalyze the coenzyme A-dependent cleavage of pyruvate to formate and acetyl-coenzyme A (CoA). Due to its extreme reactivity, the radical in PflB must be controlled carefully and, once generated, is particularly susceptible to dioxygen. Exposure to oxygen of the radical on glycine residue 734 of PflB results in cleavage of the polypeptide chain and consequent inactivation of the enzyme. Two decades ago, a small 14-kDa protein called YfiD (now called autonomous glycyl radical cofactor [GrcA]) was shown to be capable of restoring activity to O2-inactivated PflB in vitro; however, GrcA has never been shown to have this function in vivo. By constructing a strain with a chromosomally encoded PflB enzyme variant with a G734A residue exchange, we could show that cells retained near-wild type fermentative growth, as well as formate and H2 production; H2 is derived by enzymatic disproportionation of formate. Introducing a grcA deletion mutation into this strain completely prevented formate and H2 generation and reduced anaerobic growth. We could show that the conserved glycine at position 102 on GrcA was necessary for GrcA to restore PflB activity and that this recovered activity depended on the essential cysteine residues 418 and 419 in the active site of PflB. Together, our findings demonstrate that GrcA is capable of restoring in vivo activity to inactive full-length PflB and support a model whereby GrcA displaces the C-terminal glycyl radical domain to rescue the catalytic function of PflB. IMPORTANCE Many facultative anaerobic microorganisms use glycyl radical enzymes (GREs) to catalyze chemically challenging reactions under anaerobic conditions. Pyruvate formate-lyase (PflB) is a GRE that catalyzes cleavage of the carbon-carbon bond of pyruvate during glucose fermentation. The problem is that glycyl radicals are destroyed readily, especially by oxygen. To protect and restore activity to inactivated PflB, bacteria like Escherichia coli have a small autonomous glycyl radical cofactor protein called GrcA, which functions to rescue inactivated PflB. To date, this proposed function of GrcA has only been demonstrated in vitro. Our data reveal that GrcA rescues and restores enzyme activity to an inactive full-length form of PflB in vivo. These results have important implications for the evolution of radical-based enzyme mechanisms.
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16
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Lundahl MN, Sarksian R, Yang H, Jodts RJ, Pagnier A, Smith DF, Mosquera MA, van der Donk WA, Hoffman BM, Broderick WE, Broderick JB. Mechanism of Radical S-Adenosyl-l-methionine Adenosylation: Radical Intermediates and the Catalytic Competence of the 5'-Deoxyadenosyl Radical. J Am Chem Soc 2022; 144:5087-5098. [PMID: 35258967 PMCID: PMC9524473 DOI: 10.1021/jacs.1c13706] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Radical S-adenosyl-l-methionine (SAM) enzymes employ a [4Fe-4S] cluster and SAM to initiate diverse radical reactions via either H-atom abstraction or substrate adenosylation. Here we use freeze-quench techniques together with electron paramagnetic resonance (EPR) spectroscopy to provide snapshots of the reaction pathway in an adenosylation reaction catalyzed by the radical SAM enzyme pyruvate formate-lyase activating enzyme on a peptide substrate containing a dehydroalanine residue in place of the target glycine. The reaction proceeds via the initial formation of the organometallic intermediate Ω, as evidenced by the characteristic EPR signal with g∥ = 2.035 and g⊥ = 2.004 observed when the reaction is freeze-quenched at 500 ms. Thermal annealing of frozen Ω converts it into a second paramagnetic species centered at giso = 2.004; this second species was generated directly using freeze-quench at intermediate times (∼8 s) and unequivocally identified via isotopic labeling and EPR spectroscopy as the tertiary peptide radical resulting from adenosylation of the peptide substrate. An additional paramagnetic species observed in samples quenched at intermediate times was revealed through thermal annealing while frozen and spectral subtraction as the SAM-derived 5'-deoxyadenosyl radical (5'-dAdo•). The time course of the 5'-dAdo• and tertiary peptide radical EPR signals reveals that the former generates the latter. These results thus support a mechanism in which Ω liberates 5'-dAdo• by Fe-C5' bond homolysis, and the 5'-dAdo• attacks the dehydroalanine residue of the peptide substrate to form the adenosylated peptide radical species. The results thus provide a picture of a catalytically competent 5'-dAdo• intermediate trapped just prior to reaction with the substrate.
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Affiliation(s)
- Maike N. Lundahl
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717, United States
| | - Raymond Sarksian
- Department of Chemistry and Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Hao Yang
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Richard J. Jodts
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Adrien Pagnier
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717, United States
| | - Donald F. Smith
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717, United States
| | - Martín A. Mosquera
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717, United States
| | - Wilfred A. van der Donk
- Department of Chemistry and Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Brian M. Hoffman
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - William E. Broderick
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717, United States
| | - Joan B. Broderick
- Corresponding Author: Joan B. Broderick – Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717, United States;
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17
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The B 12-independent glycerol dehydratase activating enzyme from Clostridium butyricum cleaves SAM to produce 5'-deoxyadenosine and not 5'-deoxy-5'-(methylthio)adenosine. J Inorg Biochem 2022; 227:111662. [PMID: 34847521 PMCID: PMC8889718 DOI: 10.1016/j.jinorgbio.2021.111662] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Revised: 11/04/2021] [Accepted: 11/04/2021] [Indexed: 02/03/2023]
Abstract
Glycerol dehydratase activating enzyme (GD-AE) is a radical S-adenosyl-l-methionine (SAM) enzyme that installs a catalytically essential amino acid backbone radical onto glycerol dehydratase in bacteria under anaerobic conditions. Although GD-AE is closely homologous to other radical SAM activases that have been shown to cleave the S-C(5') bond of SAM to produce 5'-deoxyadenosine (5'-dAdoH) and methionine, GD-AE from Clostridium butyricum has been reported to instead cleave the S-C(γ) bond of SAM to yield 5'-deoxy-5'-(methylthio)adenosine (MTA). Here we re-investigate the SAM cleavage reaction catalyzed by GD-AE and show that it produces the widely observed 5'-dAdoH, and not the less conventional product MTA.
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18
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Rescuing activity of oxygen-damaged pyruvate formate-lyase by a spare part protein. J Biol Chem 2021; 297:101423. [PMID: 34801558 PMCID: PMC8683613 DOI: 10.1016/j.jbc.2021.101423] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Revised: 11/09/2021] [Accepted: 11/12/2021] [Indexed: 11/21/2022] Open
Abstract
Pyruvate formate-lyase (PFL) is a glycyl radical enzyme (GRE) that converts pyruvate and coenzyme A into acetyl-CoA and formate in a reaction that is crucial to the primary metabolism of many anaerobic bacteria. The glycyl radical cofactor, which is posttranslationally installed by a radical S-adenosyl-L-methionine (SAM) activase, is a simple and effective catalyst, but is also susceptible to oxidative damage in microaerobic environments. Such damage occurs at the glycyl radical cofactor, resulting in cleaved PFL (cPFL). Bacteria have evolved a spare part protein termed YfiD that can be used to repair cPFL. Previously, we obtained a structure of YfiD by NMR spectroscopy and found that the N-terminus of YfiD was disordered and that the C-terminus of YfiD duplicates the structure of the C-terminus of PFL, including a β-strand that is not removed by the oxygen-induced cleavage. We also showed that cPFL is highly susceptible to proteolysis, suggesting that YfiD rescue of cPFL competes with protein degradation. Here, we probe the mechanism by which YfiD can bind and restore activity to cPFL through enzymatic and spectroscopic studies. Our data show that the disordered N-terminal region of YfiD is important for YfiD glycyl radical installation but not for catalysis, and that the duplicate β-strand does not need to be cleaved from cPFL for YfiD to bind. In fact, truncation of this PFL region prevents YfiD rescue. Collectively our data suggest the molecular mechanisms by which YfiD activation is precluded both when PFL is not damaged and when it is highly damaged.
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19
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Tomlinson BR, Malof ME, Shaw LN. A global transcriptomic analysis of Staphylococcus aureus biofilm formation across diverse clonal lineages. Microb Genom 2021; 7. [PMID: 34227933 PMCID: PMC8477394 DOI: 10.1099/mgen.0.000598] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
A key characteristic of Staphylococcus aureus infections, and one that also varies phenotypically between clones, is that of biofilm formation, which aids in bacterial persistence through increased adherence and immune evasion. Though there is a general understanding of the process of biofilm formation - adhesion, proliferation, maturation and dispersal - the tightly orchestrated molecular events behind each stage, and what drives variation between S. aureus strains, has yet to be unravelled. Herein we measure biofilm progression and dispersal in real-time across the five major S. aureus CDC-types (USA100-USA500) revealing adherence patterns that differ markedly amongst strains. To gain insight into this, we performed transcriptomic profiling on these isolates at multiple timepoints, compared to planktonically growing counterparts. Our findings support a model in which eDNA release, followed by increased positive surface charge, perhaps drives initial abiotic attachment. This is seemingly followed by cooperative repression of autolysis and activation of poly-N-acetylglucosamine (PNAG) production, which may indicate a developmental shift in structuring the biofilm matrix. As biofilms mature, diminished translational capacity was apparent, with 53 % of all ribosomal proteins downregulated, followed by upregulation of anaerobic respiration enzymes. These findings are noteworthy because reduced cellular activity and an altered metabolic state have been previously shown to contribute to higher antibiotic tolerance and bacterial persistence. In sum, this work is, to our knowledge, the first study to investigate transcriptional regulation during the early, establishing phase of biofilm formation, and to compare global transcriptional regulation both temporally and across multiple clonal lineages.
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Affiliation(s)
- Brooke R Tomlinson
- Department of Cell Biology, Microbiology and Molecular Biology, University of South Florida, 4202 East Fowler Avenue, ISA 2015, Tampa, FL, USA
| | - Morgan E Malof
- Department of Cell Biology, Microbiology and Molecular Biology, University of South Florida, 4202 East Fowler Avenue, ISA 2015, Tampa, FL, USA
| | - Lindsey N Shaw
- Department of Cell Biology, Microbiology and Molecular Biology, University of South Florida, 4202 East Fowler Avenue, ISA 2015, Tampa, FL, USA
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20
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Tomlinson BR, Malof ME, Shaw LN. A global transcriptomic analysis of Staphylococcus aureus biofilm formation across diverse clonal lineages. Microb Genom 2021. [PMID: 34227933 DOI: 10.1099/mgen0000598] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2023] Open
Abstract
A key characteristic of Staphylococcus aureus infections, and one that also varies phenotypically between clones, is that of biofilm formation, which aids in bacterial persistence through increased adherence and immune evasion. Though there is a general understanding of the process of biofilm formation - adhesion, proliferation, maturation and dispersal - the tightly orchestrated molecular events behind each stage, and what drives variation between S. aureus strains, has yet to be unravelled. Herein we measure biofilm progression and dispersal in real-time across the five major S. aureus CDC-types (USA100-USA500) revealing adherence patterns that differ markedly amongst strains. To gain insight into this, we performed transcriptomic profiling on these isolates at multiple timepoints, compared to planktonically growing counterparts. Our findings support a model in which eDNA release, followed by increased positive surface charge, perhaps drives initial abiotic attachment. This is seemingly followed by cooperative repression of autolysis and activation of poly-N-acetylglucosamine (PNAG) production, which may indicate a developmental shift in structuring the biofilm matrix. As biofilms mature, diminished translational capacity was apparent, with 53 % of all ribosomal proteins downregulated, followed by upregulation of anaerobic respiration enzymes. These findings are noteworthy because reduced cellular activity and an altered metabolic state have been previously shown to contribute to higher antibiotic tolerance and bacterial persistence. In sum, this work is, to our knowledge, the first study to investigate transcriptional regulation during the early, establishing phase of biofilm formation, and to compare global transcriptional regulation both temporally and across multiple clonal lineages.
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Affiliation(s)
- Brooke R Tomlinson
- Department of Cell Biology, Microbiology and Molecular Biology, University of South Florida, 4202 East Fowler Avenue, ISA 2015, Tampa, FL, USA
| | - Morgan E Malof
- Department of Cell Biology, Microbiology and Molecular Biology, University of South Florida, 4202 East Fowler Avenue, ISA 2015, Tampa, FL, USA
| | - Lindsey N Shaw
- Department of Cell Biology, Microbiology and Molecular Biology, University of South Florida, 4202 East Fowler Avenue, ISA 2015, Tampa, FL, USA
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21
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Adenosylation reactions catalyzed by the radical S-adenosylmethionine superfamily enzymes. Curr Opin Chem Biol 2020; 55:86-95. [DOI: 10.1016/j.cbpa.2020.01.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 12/22/2019] [Accepted: 01/15/2020] [Indexed: 01/23/2023]
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22
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A lipophilic cation protects crops against fungal pathogens by multiple modes of action. Nat Commun 2020; 11:1608. [PMID: 32231209 PMCID: PMC7105494 DOI: 10.1038/s41467-020-14949-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 02/11/2020] [Indexed: 12/21/2022] Open
Abstract
The emerging resistance of crop pathogens to fungicides poses a challenge to food security and compels discovery of new antifungal compounds. Here, we show that mono-alkyl lipophilic cations (MALCs) inhibit oxidative phosphorylation by affecting NADH oxidation in the plant pathogens Zymoseptoria tritici, Ustilago maydis and Magnaporthe oryzae. One of these MALCs, consisting of a dimethylsulfonium moiety and a long alkyl chain (C18-SMe2+), also induces production of reactive oxygen species at the level of respiratory complex I, thus triggering fungal apoptosis. In addition, C18-SMe2+ activates innate plant defense. This multiple activity effectively protects cereals against Septoria tritici blotch and rice blast disease. C18-SMe2+ has low toxicity in Daphnia magna, and is not mutagenic or phytotoxic. Thus, MALCs hold potential as effective and non-toxic crop fungicides. New fungicides are needed due to emerging resistance shown by crop pathogens. Here, the authors show that a mono-alkyl lipophilic cation protects plants from fungal pathogens by inhibiting fungal mitochondrial respiration, inducing production of reactive oxygen species, triggering fungal apoptosis, and activating innate plant defense.
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23
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Backman LRF, Huang YY, Andorfer MC, Gold B, Raines RT, Balskus EP, Drennan CL. Molecular basis for catabolism of the abundant metabolite trans-4-hydroxy-L-proline by a microbial glycyl radical enzyme. eLife 2020; 9:e51420. [PMID: 32180548 PMCID: PMC7077986 DOI: 10.7554/elife.51420] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 02/19/2020] [Indexed: 02/04/2023] Open
Abstract
The glycyl radical enzyme (GRE) superfamily utilizes a glycyl radical cofactor to catalyze difficult chemical reactions in a variety of anaerobic microbial metabolic pathways. Recently, a GRE, trans-4-hydroxy-L-proline (Hyp) dehydratase (HypD), was discovered that catalyzes the dehydration of Hyp to (S)-Δ1-pyrroline-5-carboxylic acid (P5C). This enzyme is abundant in the human gut microbiome and also present in prominent bacterial pathogens. However, we lack an understanding of how HypD performs its unusual chemistry. Here, we have solved the crystal structure of HypD from the pathogen Clostridioides difficile with Hyp bound in the active site. Biochemical studies have led to the identification of key catalytic residues and have provided insight into the radical mechanism of Hyp dehydration.
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Affiliation(s)
- Lindsey RF Backman
- Department of Chemistry, Massachusetts Institute of TechnologyCambridgeUnited States
| | - Yolanda Y Huang
- Department of Chemistry and Chemical Biology, Harvard UniversityCambridgeUnited States
| | - Mary C Andorfer
- Department of Biology, Massachusetts Institute of TechnologyCambridgeUnited States
| | - Brian Gold
- Department of Chemistry, Massachusetts Institute of TechnologyCambridgeUnited States
| | - Ronald T Raines
- Department of Chemistry, Massachusetts Institute of TechnologyCambridgeUnited States
| | - Emily P Balskus
- Department of Chemistry and Chemical Biology, Harvard UniversityCambridgeUnited States
| | - Catherine L Drennan
- Department of Chemistry, Massachusetts Institute of TechnologyCambridgeUnited States
- Department of Biology, Massachusetts Institute of TechnologyCambridgeUnited States
- Howard Hughes Medical Institute, Massachusetts Institute of TechnologyCambridgeUnited States
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24
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Yang H, Impano S, Shepard EM, James CD, Broderick WE, Broderick JB, Hoffman BM. Photoinduced Electron Transfer in a Radical SAM Enzyme Generates an S-Adenosylmethionine Derived Methyl Radical. J Am Chem Soc 2019; 141:16117-16124. [PMID: 31509404 DOI: 10.1021/jacs.9b08541] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Radical SAM (RS) enzymes use S-adenosyl-l-methionine (SAM) and a [4Fe-4S] cluster to initiate a broad spectrum of radical transformations throughout all kingdoms of life. We report here that low-temperature photoinduced electron transfer from the [4Fe-4S]1+ cluster to bound SAM in the active site of the hydrogenase maturase RS enzyme, HydG, results in specific homolytic cleavage of the S-CH3 bond of SAM, rather than the S-C5' bond as in the enzyme-catalyzed (thermal) HydG reaction. This result is in stark contrast to a recent report in which photoinduced ET in the RS enzyme pyruvate formate-lyase activating enzyme cleaved the S-C5' bond to generate a 5'-deoxyadenosyl radical, and provides the first direct evidence for homolytic S-CH3 bond cleavage in a RS enzyme. Photoinduced ET in HydG generates a trapped •CH3 radical, as well as a small population of an organometallic species with an Fe-CH3 bond, denoted ΩM. The •CH3 radical is surprisingly found to exhibit rotational diffusion in the HydG active site at temperatures as low as 40 K, and is rapidly quenched: whereas 5'-dAdo• is stable indefinitely at 77 K, •CH3 quenches with a half-time of ∼2 min at this temperature. The rapid quenching and rotational/translational freedom of •CH3 shows that enzymes would be unable to harness this radical as a regio- and stereospecific H atom abstractor during catalysis, in contrast to the exquisite control achieved with the enzymatically generated 5'-dAdo•.
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Affiliation(s)
- Hao Yang
- Department of Chemistry , Northwestern University , Evanston , Illinois 60208 , United States
| | - Stella Impano
- Department of Chemistry & Biochemistry , Montana State University , Bozeman , Montana 59717 , United States
| | - Eric M Shepard
- Department of Chemistry & Biochemistry , Montana State University , Bozeman , Montana 59717 , United States
| | - Christopher D James
- Department of Chemistry , Northwestern University , Evanston , Illinois 60208 , United States
| | - William E Broderick
- Department of Chemistry & Biochemistry , Montana State University , Bozeman , Montana 59717 , United States
| | - Joan B Broderick
- Department of Chemistry & Biochemistry , Montana State University , Bozeman , Montana 59717 , United States
| | - Brian M Hoffman
- Department of Chemistry , Northwestern University , Evanston , Illinois 60208 , United States
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25
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Yang H, McDaniel EC, Impano S, Byer AS, Jodts RJ, Yokoyama K, Broderick WE, Broderick JB, Hoffman BM. The Elusive 5'-Deoxyadenosyl Radical: Captured and Characterized by Electron Paramagnetic Resonance and Electron Nuclear Double Resonance Spectroscopies. J Am Chem Soc 2019; 141:12139-12146. [PMID: 31274303 DOI: 10.1021/jacs.9b05926] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The 5'-deoxyadenosyl radical (5'-dAdo·) abstracts a substrate H atom as the first step in radical-based transformations catalyzed by adenosylcobalamin-dependent and radical S-adenosyl-l-methionine (RS) enzymes. Notwithstanding its central biological role, 5'-dAdo· has eluded characterization despite efforts spanning more than a half-century. Here, we report generation of 5'-dAdo· in a RS enzyme active site at 12 K using a novel approach involving cryogenic photoinduced electron transfer from the [4Fe-4S]+ cluster to the coordinated S-adenosylmethionine (SAM) to induce homolytic S-C5' bond cleavage. We unequivocally reveal the structure of this long-sought radical species through the use of electron paramagnetic resonance (EPR) and electron nuclear double resonance (ENDOR) spectroscopies with isotopic labeling, complemented by density-functional computations: a planar C5' (2pπ) radical (∼70% spin occupancy); the C5'(H)2 plane is rotated by ∼37° (experiment)/39° (DFT) relative to the C5'-C4'-(C4'-H) plane, placing a C5'-H antiperiplanar to the ribose-ring oxygen, which helps stabilize the radical against elimination of the 4'-H. The agreement between φ from experiment and in vacuo DFT indicates that the conformation is intrinsic to 5-dAdo· itself, and not determined by its environment.
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Affiliation(s)
- Hao Yang
- Department of Chemistry , Northwestern University , Evanston , Illinois 60208 , United States
| | - Elizabeth C McDaniel
- Department of Chemistry and Biochemistry , Montana State University , Bozeman , Montana 59717 , United States
| | - Stella Impano
- Department of Chemistry and Biochemistry , Montana State University , Bozeman , Montana 59717 , United States
| | - Amanda S Byer
- Department of Chemistry and Biochemistry , Montana State University , Bozeman , Montana 59717 , United States
| | - Richard J Jodts
- Department of Chemistry , Northwestern University , Evanston , Illinois 60208 , United States
| | - Kenichi Yokoyama
- Department of Biochemistry , Duke University , Durham , North Carolina 27710 , United States
| | - William E Broderick
- Department of Chemistry and Biochemistry , Montana State University , Bozeman , Montana 59717 , United States
| | - Joan B Broderick
- Department of Chemistry and Biochemistry , Montana State University , Bozeman , Montana 59717 , United States
| | - Brian M Hoffman
- Department of Chemistry , Northwestern University , Evanston , Illinois 60208 , United States
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Bilić L, Barić D, Banhatti RD, Smith DM, Kovačević B. Computational Study of Glycerol Binding within the Active Site of Coenzyme B12-Dependent Diol Dehydratase. J Phys Chem B 2019; 123:6178-6187. [DOI: 10.1021/acs.jpcb.9b04071] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Luka Bilić
- Division of Physical Chemistry, Rud̵er Bošković Institute, Bijenička 54, 10000 Zagreb, Croatia
| | - Danijela Barić
- Division of Physical Chemistry, Rud̵er Bošković Institute, Bijenička 54, 10000 Zagreb, Croatia
| | - Radha Dilip Banhatti
- Division of Physical Chemistry, Rud̵er Bošković Institute, Bijenička 54, 10000 Zagreb, Croatia
| | - David M. Smith
- Division of Physical Chemistry, Rud̵er Bošković Institute, Bijenička 54, 10000 Zagreb, Croatia
| | - Borislav Kovačević
- Division of Physical Chemistry, Rud̵er Bošković Institute, Bijenička 54, 10000 Zagreb, Croatia
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27
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Hanževački M, Čondić-Jurkić K, Banhatti RD, Smith AS, Smith DM. The Influence of Chemical Change on Protein Dynamics: A Case Study with Pyruvate Formate-Lyase. Chemistry 2019; 25:8741-8753. [PMID: 30901109 DOI: 10.1002/chem.201900663] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Indexed: 12/15/2022]
Abstract
Pyruvate formate-lyase (PFL) catalyzes the reversible conversion of pyruvate and coenzyme A (CoA) into formate and acetyl-CoA in two half-reactions. For the second half-reaction to take place, the S-H group of CoA must enter the active site of the enzyme to retrieve a protein-bound acetyl group. However, CoA is bound at the protein surface, whereas the active site is buried in the protein interior, some 20-30 Å away. The PFL system was therefore subjected to a series of extensive molecular dynamics simulations (in the μs range) and a host of advanced analysis procedures. Models representing PFL before and after the first half-reaction were used to examine the possible effect of enzyme acetylation. All simulated structures were found to be relatively stable compared to the initial crystal structure. Although the adenine portion of CoA remained predominantly bound at the protein surface, the binding of the S-H group was significantly more labile. A potential entry channel for CoA, which would allow the S-H group to reach the active site, was identified and characterized. The channel was found to be associated with accentuated fluctuations and a higher probability of being in an open state in acetylated systems. This result suggests that the acetylation of the enzyme assumes a prominent functional role, whereby the formation of the acyl intermediate serves to initiate a subtle signaling cascade that influences the protein dynamics and facilitates the entry of the second substrate.
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Affiliation(s)
- Marko Hanževački
- Division of Physical Chemistry, Ruđer Bošković Institute, Bijenička 54, Zagreb, Croatia.,PULS Group, Institute for Theoretical Physics, FAU Erlangen-Nürnberg, Staudtstraße 7, Erlangen, Germany
| | - Karmen Čondić-Jurkić
- Division of Physical Chemistry, Ruđer Bošković Institute, Bijenička 54, Zagreb, Croatia
| | - Radha Dilip Banhatti
- Division of Physical Chemistry, Ruđer Bošković Institute, Bijenička 54, Zagreb, Croatia
| | - Ana-Sunčana Smith
- Division of Physical Chemistry, Ruđer Bošković Institute, Bijenička 54, Zagreb, Croatia.,PULS Group, Institute for Theoretical Physics, FAU Erlangen-Nürnberg, Staudtstraße 7, Erlangen, Germany
| | - David M Smith
- Division of Physical Chemistry, Ruđer Bošković Institute, Bijenička 54, Zagreb, Croatia
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Broderick WE, Hoffman BM, Broderick JB. Mechanism of Radical Initiation in the Radical S-Adenosyl-l-methionine Superfamily. Acc Chem Res 2018; 51:2611-2619. [PMID: 30346729 PMCID: PMC6324848 DOI: 10.1021/acs.accounts.8b00356] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The seeds for recognition of the vast superfamily of radical S-adenosyl-l-methionine (SAM) enzymes were sown in the 1960s, when Joachim Knappe found that the dissimilation of pyruvate was dependent on SAM and Fe(II), and Barker and co-workers made similar observations for lysine 2,3-aminomutase. These intriguing observations, coupled with the evidence that SAM and Fe were cofactors in radical catalysis by these enzyme systems, drew us in the 1990s to explore how Fe(II) and SAM initiate radical reactions. Our early work focused on the same enzyme Knappe had originally characterized: the pyruvate formate-lyase activating enzyme (PFL-AE). Our discovery of an iron-sulfur cluster in this enzyme, together with similar findings for other SAM-dependent enzymes at the time, led to the recognition of an emerging class of enzymes that use iron-sulfur clusters to cleave SAM, liberating the 5'-deoxyadenosyl radical (5'-dAdo•) that initiates radical reactions. A major bioinformatics study by Heidi Sofia and co-workers identified the enzyme superfamily denoted Radical SAM, now known to span all kingdoms of life with more than 100,000 unique sequences encoding enzymes that catalyze remarkably diverse reactions. Despite the limited sequence similarity and vastly divergent reactions catalyzed, the radical SAM enzymes appear to employ a common mechanism for initiation of radical chemistry, a mechanism we have helped to clarify over the last 25 years. A reduced [4Fe-4S]+ cluster provides the electron needed for the reductive cleavage of SAM. The resulting [4Fe-4S]2+ cluster can be rereduced either by an external reductant, with SAM acting as a cosubstrate, or by an electron provided during the reformation of SAM in cases where SAM is used as a cofactor. The amino and carboxylate groups of SAM bind to the unique iron of the catalytic [4Fe-4S] cluster, placing the sulfonium of SAM in close proximity to the cluster. Surprising recent results have shown that the initiating enzymatic cleavage of SAM generates an organometallic intermediate prior to liberation of 5'-dAdo•, which initiates radical chemistry on the substrate. This organometallic intermediate, denoted Ω, has a 5'-deoxyadenosyl moiety directly bound to the unique iron of the [4Fe-4S] cluster via the 5'-C, giving a structure that is directly analogous to the Co-(5'-C) bond of the organometallic cofactor adenosylcobalamin. Our observation that this intermediate Ω is formed throughout the superfamily suggests that this is a key intermediate in initiating radical SAM reactions, and that organometallic chemistry is much more broadly relevant in biology than previously thought.
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Affiliation(s)
- William E. Broderick
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717, United States
| | - Brian M. Hoffman
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Joan B. Broderick
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717, United States,Corresponding Author, .
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29
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Byer A, Yang H, McDaniel EC, Kathiresan V, Impano S, Pagnier A, Watts H, Denler C, Vagstad AL, Piel J, Duschene KS, Shepard EM, Shields TP, Scott LG, Lilla EA, Yokoyama K, Broderick WE, Hoffman BM, Broderick JB. Paradigm Shift for Radical S-Adenosyl-l-methionine Reactions: The Organometallic Intermediate Ω Is Central to Catalysis. J Am Chem Soc 2018; 140:8634-8638. [PMID: 29954180 PMCID: PMC6053644 DOI: 10.1021/jacs.8b04061] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
Radical S-adenosyl-l-methionine (SAM) enzymes comprise a vast superfamily catalyzing diverse reactions essential to all life through homolytic SAM cleavage to liberate the highly reactive 5'-deoxyadenosyl radical (5'-dAdo·). Our recent observation of a catalytically competent organometallic intermediate Ω that forms during reaction of the radical SAM (RS) enzyme pyruvate formate-lyase activating-enzyme (PFL-AE) was therefore quite surprising, and led to the question of its broad relevance in the superfamily. We now show that Ω in PFL-AE forms as an intermediate under a variety of mixing order conditions, suggesting it is central to catalysis in this enzyme. We further demonstrate that Ω forms in a suite of RS enzymes chosen to span the totality of superfamily reaction types, implicating Ω as essential in catalysis across the RS superfamily. Finally, EPR and electron nuclear double resonance spectroscopy establish that Ω involves an Fe-C5' bond between 5'-dAdo· and the [4Fe-4S] cluster. An analogous organometallic bond is found in the well-known adenosylcobalamin (coenzyme B12) cofactor used to initiate radical reactions via a 5'-dAdo· intermediate. Liberation of a reactive 5'-dAdo· intermediate via homolytic metal-carbon bond cleavage thus appears to be similar for Ω and coenzyme B12. However, coenzyme B12 is involved in enzymes catalyzing only a small number (∼12) of distinct reactions, whereas the RS superfamily has more than 100 000 distinct sequences and over 80 reaction types characterized to date. The appearance of Ω across the RS superfamily therefore dramatically enlarges the sphere of bio-organometallic chemistry in Nature.
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Affiliation(s)
- Amanda
S. Byer
- Department
of Chemistry & Biochemistry, Montana
State University, Bozeman, Montana 59717, United States
| | - Hao Yang
- Department
of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Elizabeth C. McDaniel
- Department
of Chemistry & Biochemistry, Montana
State University, Bozeman, Montana 59717, United States
| | - Venkatesan Kathiresan
- Department
of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Stella Impano
- Department
of Chemistry & Biochemistry, Montana
State University, Bozeman, Montana 59717, United States
| | - Adrien Pagnier
- Department
of Chemistry & Biochemistry, Montana
State University, Bozeman, Montana 59717, United States
| | - Hope Watts
- Department
of Chemistry & Biochemistry, Montana
State University, Bozeman, Montana 59717, United States
| | - Carly Denler
- Department
of Chemistry & Biochemistry, Montana
State University, Bozeman, Montana 59717, United States
| | - Anna L. Vagstad
- Institute
of Microbiology, Eidgenössische Technische
Hochschule Zürich, Vladimir-Prelog-Weg 4, Zürich 8093, Switzerland
| | - Jörn Piel
- Institute
of Microbiology, Eidgenössische Technische
Hochschule Zürich, Vladimir-Prelog-Weg 4, Zürich 8093, Switzerland
| | - Kaitlin S. Duschene
- Department
of Chemistry & Biochemistry, Montana
State University, Bozeman, Montana 59717, United States
| | - Eric M. Shepard
- Department
of Chemistry & Biochemistry, Montana
State University, Bozeman, Montana 59717, United States
| | - Thomas P. Shields
- Cassia,
LLC, 3030 Bunker Hill
Street, Ste. 214, San Diego, California 92109, United States
| | - Lincoln G. Scott
- Cassia,
LLC, 3030 Bunker Hill
Street, Ste. 214, San Diego, California 92109, United States
| | - Edward A. Lilla
- Department
of Biochemistry, Duke University Medical
Center, Durham, North Carolina 27710, United States
| | - Kenichi Yokoyama
- Department
of Biochemistry, Duke University Medical
Center, Durham, North Carolina 27710, United States
| | - William E. Broderick
- Department
of Chemistry & Biochemistry, Montana
State University, Bozeman, Montana 59717, United States
| | - Brian M. Hoffman
- Department
of Chemistry, Northwestern University, Evanston, Illinois 60208, United States,
| | - Joan B. Broderick
- Department
of Chemistry & Biochemistry, Montana
State University, Bozeman, Montana 59717, United States,
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30
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Kovačević B, Barić D, Babić D, Bilić L, Hanževački M, Sandala GM, Radom L, Smith DM. Computational Tale of Two Enzymes: Glycerol Dehydration With or Without B12. J Am Chem Soc 2018; 140:8487-8496. [DOI: 10.1021/jacs.8b03109] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Borislav Kovačević
- Department of Physical Chemistry, Ruđer Bošković Institute, 10000 Zagreb, Croatia
| | - Danijela Barić
- Department of Physical Chemistry, Ruđer Bošković Institute, 10000 Zagreb, Croatia
| | - Darko Babić
- Department of Physical Chemistry, Ruđer Bošković Institute, 10000 Zagreb, Croatia
| | - Luka Bilić
- Department of Physical Chemistry, Ruđer Bošković Institute, 10000 Zagreb, Croatia
| | - Marko Hanževački
- Department of Physical Chemistry, Ruđer Bošković Institute, 10000 Zagreb, Croatia
| | - Gregory M. Sandala
- Department of Chemistry and Biochemistry, Mount Allison University, Sackville, New Brunswick E4L 1G8, Canada
| | - Leo Radom
- School of Chemistry, University of Sydney, Sydney, NSW 2006, Australia
| | - David M. Smith
- Department of Physical Chemistry, Ruđer Bošković Institute, 10000 Zagreb, Croatia
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31
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Byer AS, McDaniel EC, Impano S, Broderick WE, Broderick JB. Mechanistic Studies of Radical SAM Enzymes: Pyruvate Formate-Lyase Activating Enzyme and Lysine 2,3-Aminomutase Case Studies. Methods Enzymol 2018; 606:269-318. [DOI: 10.1016/bs.mie.2018.04.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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32
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Berteau O, Benjdia A. DNA Repair by the Radical SAM Enzyme Spore Photoproduct Lyase: From Biochemistry to Structural Investigations. Photochem Photobiol 2017; 93:67-77. [DOI: 10.1111/php.12702] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Accepted: 12/19/2016] [Indexed: 10/20/2022]
Affiliation(s)
- Olivier Berteau
- Micalis Institute; INRA; ChemSyBio; AgroParisTech; Université Paris-Saclay; Jouy-en-Josas France
| | - Alhosna Benjdia
- Micalis Institute; INRA; ChemSyBio; AgroParisTech; Université Paris-Saclay; Jouy-en-Josas France
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33
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LaMattina JW, Keul ND, Reitzer P, Kapoor S, Galzerani F, Koch DJ, Gouvea IE, Lanzilotta WN. 1,2-Propanediol Dehydration in Roseburia inulinivorans: STRUCTURAL BASIS FOR SUBSTRATE AND ENANTIOMER SELECTIVITY. J Biol Chem 2016; 291:15515-26. [PMID: 27252380 DOI: 10.1074/jbc.m116.721142] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Indexed: 11/06/2022] Open
Abstract
Glycyl radical enzymes (GREs) represent a diverse superfamily of enzymes that utilize a radical mechanism to catalyze difficult, but often essential, chemical reactions. In this work we present the first biochemical and structural data for a GRE-type diol dehydratase from the organism Roseburia inulinivorans (RiDD). Despite high sequence (48% identity) and structural similarity to the GRE-type glycerol dehydratase from Clostridium butyricum, we demonstrate that the RiDD is in fact a diol dehydratase. In addition, the RiDD will utilize both (S)-1,2-propanediol and (R)-1,2-propanediol as a substrate, with an observed preference for the S enantiomer. Based on the new structural information we developed and successfully tested a hypothesis that explains the functional differences we observe.
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Affiliation(s)
- Joseph W LaMattina
- From the Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602 and
| | - Nicholas D Keul
- From the Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602 and
| | - Pierre Reitzer
- From the Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602 and
| | - Suraj Kapoor
- From the Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602 and
| | - Felipe Galzerani
- BRASKEM S.A., Rua Lemos Moonteiro, 120 Edifício Odebrecht São Paulo, Butantã 05501-050-São Paulo, SP Brasil
| | - Daniel J Koch
- BRASKEM S.A., Rua Lemos Moonteiro, 120 Edifício Odebrecht São Paulo, Butantã 05501-050-São Paulo, SP Brasil
| | - Iuri E Gouvea
- BRASKEM S.A., Rua Lemos Moonteiro, 120 Edifício Odebrecht São Paulo, Butantã 05501-050-São Paulo, SP Brasil
| | - William N Lanzilotta
- From the Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602 and
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Abstract
Pyruvate and acetyl-CoA form the backbone of central metabolism. The nonoxidative cleavage of pyruvate to acetyl-CoA and formate by the glycyl radical enzyme pyruvate formate lyase is one of the signature reactions of mixed-acid fermentation in enterobacteria. Under these conditions, formic acid accounts for up to one-third of the carbon derived from glucose. The further metabolism of acetyl-CoA to acetate via acetyl-phosphate catalyzed by phosphotransacetylase and acetate kinase is an exemplar of substrate-level phosphorylation. Acetyl-CoA can also be used as an acceptor of the reducing equivalents generated during glycolysis, whereby ethanol is formed by the polymeric acetaldehyde/alcohol dehydrogenase (AdhE) enzyme. The metabolism of acetyl-CoA via either the acetate or the ethanol branches is governed by the cellular demand for ATP and the necessity to reoxidize NADH. Consequently, in the absence of an electron acceptor mutants lacking either branch of acetyl-CoA metabolism fail to cleave pyruvate, despite the presence of PFL, and instead reduce it to D-lactate by the D-lactate dehydrogenase. The conversion of PFL to the active, radical-bearing species is controlled by a radical-SAM enzyme, PFL-activase. All of these reactions are regulated in response to the prevalent cellular NADH:NAD+ ratio. In contrast to Escherichia coli and Salmonella species, some genera of enterobacteria, e.g., Klebsiella and Enterobacter, produce the more neutral product 2,3-butanediol and considerable amounts of CO2 as fermentation products. In these bacteria, two molecules of pyruvate are converted to α-acetolactate (AL) by α-acetolactate synthase (ALS). AL is then decarboxylated and subsequently reduced to the product 2,3-butandiol.
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35
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Bioinformatic characterization of glycyl radical enzyme-associated bacterial microcompartments. Appl Environ Microbiol 2015; 81:8315-29. [PMID: 26407889 DOI: 10.1128/aem.02587-15] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2015] [Accepted: 09/18/2015] [Indexed: 12/26/2022] Open
Abstract
Bacterial microcompartments (BMCs) are proteinaceous organelles encapsulating enzymes that catalyze sequential reactions of metabolic pathways. BMCs are phylogenetically widespread; however, only a few BMCs have been experimentally characterized. Among them are the carboxysomes and the propanediol- and ethanolamine-utilizing microcompartments, which play diverse metabolic and ecological roles. The substrate of a BMC is defined by its signature enzyme. In catabolic BMCs, this enzyme typically generates an aldehyde. Recently, it was shown that the most prevalent signature enzymes encoded by BMC loci are glycyl radical enzymes, yet little is known about the function of these BMCs. Here we characterize the glycyl radical enzyme-associated microcompartment (GRM) loci using a combination of bioinformatic analyses and active-site and structural modeling to show that the GRMs comprise five subtypes. We predict distinct functions for the GRMs, including the degradation of choline, propanediol, and fuculose phosphate. This is the first family of BMCs for which identification of the signature enzyme is insufficient for predicting function. The distinct GRM functions are also reflected in differences in shell composition and apparently different assembly pathways. The GRMs are the counterparts of the vitamin B12-dependent propanediol- and ethanolamine-utilizing BMCs, which are frequently associated with virulence. This study provides a comprehensive foundation for experimental investigations of the diverse roles of GRMs. Understanding this plasticity of function within a single BMC family, including characterization of differences in permeability and assembly, can inform approaches to BMC bioengineering and the design of therapeutics.
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36
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Shibata N, Toraya T. Molecular architectures and functions of radical enzymes and their (re)activating proteins. J Biochem 2015; 158:271-92. [PMID: 26261050 DOI: 10.1093/jb/mvv078] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Accepted: 07/22/2015] [Indexed: 02/07/2023] Open
Abstract
Certain proteins utilize the high reactivity of radicals for catalysing chemically challenging reactions. These proteins contain or form a radical and therefore named 'radical enzymes'. Radicals are introduced by enzymes themselves or by (re)activating proteins called (re)activases. The X-ray structures of radical enzymes and their (re)activases revealed some structural features of these molecular apparatuses which solved common enigmas of radical enzymes—i.e. how the enzymes form or introduce radicals at the active sites, how they use the high reactivity of radicals for catalysis, how they suppress undesired side reactions of highly reactive radicals and how they are (re)activated when inactivated by extinction of radicals. This review highlights molecular architectures of radical B12 enzymes, radical SAM enzymes, tyrosyl radical enzymes, glycyl radical enzymes and their (re)activating proteins that support their functions. For generalization, comparisons of the recently reported structures of radical enzymes with those of canonical radical enzymes are summarized here.
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Affiliation(s)
- Naoki Shibata
- Department of Life Science, Graduate School of Life Science, University of Hyogo, 3-2-1 Koto, Kamigori-cho, Ako-gun, Hyogo 678-1297, Japan and
| | - Tetsuo Toraya
- Department of Bioscience and Biotechnology, Graduate School of Natural Science and Technology, Okayama University, Tsushima-naka, Kita-ku, Okayama 700-8530, Japan
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37
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Mahoney JK, Martin D, Thomas F, Moore CE, Rheingold AL, Bertrand G. Air-persistent monomeric (amino)(carboxy) radicals derived from cyclic (alkyl)(amino) carbenes. J Am Chem Soc 2015; 137:7519-25. [PMID: 26011769 DOI: 10.1021/jacs.5b04414] [Citation(s) in RCA: 88] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
A series of monomeric (amino)(carboxy) radicals featuring carbonyl substituents with increasing electron-withdrawing properties (3a, phenyl; 3b, 3,5-bis(trifluoromethyl)phenyl; 3c, perfluorophenyl; 3d, heptafluoropropyl; 3e, 2H-pyrroliumyl) were synthesized in two or three steps from stable cyclic (alky)(amino)carbenes (CAACs). Although (amino)(carboxy) radicals had been previously considered as highly air-sensitive, some of these compounds feature half-lives of hours (3d), and even days (3c and 3e) in well-aerated solutions. DFT calculations show that (amino)(carboxy) radicals evolve from C-centered radical to ambidentate C,O-radicals when increasing the electron-withdrawing properties of the carbonyl substituent. This is paralleled with a destabilization of the peroxide resulting from the addition of dioxygen to the radical. This latter reaction is even predicted to be endothermic for substituents with Hammett constant σp > 0.2.
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Affiliation(s)
- Janell K Mahoney
- †UCSD-CNRS Joint Research Laboratory (UMI 3555), Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093-0343, United States
| | - David Martin
- †UCSD-CNRS Joint Research Laboratory (UMI 3555), Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093-0343, United States.,‡UMR CNRS 5250, Département de Chimie Moléculaire, Université Joseph Fourier B. P. 53, 38041 Cedex 9 Grenoble, France
| | - Fabrice Thomas
- ‡UMR CNRS 5250, Département de Chimie Moléculaire, Université Joseph Fourier B. P. 53, 38041 Cedex 9 Grenoble, France
| | - Curtis E Moore
- §UCSD Crystallography Facility, San Diego, La Jolla, California 92093-0343, United States
| | - Arnold L Rheingold
- §UCSD Crystallography Facility, San Diego, La Jolla, California 92093-0343, United States
| | - Guy Bertrand
- †UCSD-CNRS Joint Research Laboratory (UMI 3555), Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093-0343, United States
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38
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Zhang Y, Dai Z, Krivoruchko A, Chen Y, Siewers V, Nielsen J. Functional pyruvate formate lyase pathway expressed with two different electron donors in Saccharomyces cerevisiae at aerobic growth. FEMS Yeast Res 2015; 15:fov024. [DOI: 10.1093/femsyr/fov024] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/10/2015] [Indexed: 11/14/2022] Open
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Lundin D, Berggren G, Logan DT, Sjöberg BM. The origin and evolution of ribonucleotide reduction. Life (Basel) 2015; 5:604-36. [PMID: 25734234 PMCID: PMC4390871 DOI: 10.3390/life5010604] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Revised: 02/04/2015] [Accepted: 02/06/2015] [Indexed: 11/16/2022] Open
Abstract
Ribonucleotide reduction is the only pathway for de novo synthesis of deoxyribonucleotides in extant organisms. This chemically demanding reaction, which proceeds via a carbon-centered free radical, is catalyzed by ribonucleotide reductase (RNR). The mechanism has been deemed unlikely to be catalyzed by a ribozyme, creating an enigma regarding how the building blocks for DNA were synthesized at the transition from RNA- to DNA-encoded genomes. While it is entirely possible that a different pathway was later replaced with the modern mechanism, here we explore the evolutionary and biochemical limits for an origin of the mechanism in the RNA + protein world and suggest a model for a prototypical ribonucleotide reductase (protoRNR). From the protoRNR evolved the ancestor to modern RNRs, the urRNR, which diversified into the modern three classes. Since the initial radical generation differs between the three modern classes, it is difficult to establish how it was generated in the urRNR. Here we suggest a model that is similar to the B12-dependent mechanism in modern class II RNRs.
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Affiliation(s)
- Daniel Lundin
- Department of Biochemistry and Biophysics, Arrhenius Laboratories, Stockholm University, SE-106 91 Stockholm, Sweden.
| | - Gustav Berggren
- Department of Biochemistry and Biophysics, Arrhenius Laboratories, Stockholm University, SE-106 91 Stockholm, Sweden.
| | - Derek T Logan
- Department of Biochemistry and Structural Biology, Lund University, Box 124, SE-221 00 Lund, Sweden.
| | - Britt-Marie Sjöberg
- Department of Biochemistry and Biophysics, Arrhenius Laboratories, Stockholm University, SE-106 91 Stockholm, Sweden.
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40
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Williamson HR, Dow BA, Davidson VL. Mechanisms for control of biological electron transfer reactions. Bioorg Chem 2014; 57:213-221. [PMID: 25085775 PMCID: PMC4285783 DOI: 10.1016/j.bioorg.2014.06.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2014] [Revised: 06/17/2014] [Accepted: 06/20/2014] [Indexed: 10/25/2022]
Abstract
Electron transfer (ET) through and between proteins is a fundamental biological process. The rates and mechanisms of these ET reactions are controlled by the proteins in which the redox centers that donate and accept electrons reside. The protein influences the magnitudes of the ET parameters, the electronic coupling and reorganization energy that are associated with the ET reaction. The protein can regulate the rates of the ET reaction by requiring reaction steps to optimize the system for ET, leading to kinetic mechanisms of gated or coupled ET. Amino acid residues in the segment of the protein through which long range ET occurs can also modulate the ET rate by serving as staging points for hopping mechanisms of ET. Specific examples are presented to illustrate these mechanisms by which proteins control rates of ET reactions.
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Affiliation(s)
- Heather R Williamson
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL 32827, United States
| | - Brian A Dow
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL 32827, United States
| | - Victor L Davidson
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL 32827, United States.
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41
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Thompson MC, Wheatley NM, Jorda J, Sawaya MR, Gidaniyan SD, Ahmed H, Yang Z, McCarty KN, Whitelegge JP, Yeates TO. Identification of a unique Fe-S cluster binding site in a glycyl-radical type microcompartment shell protein. J Mol Biol 2014; 426:3287-3304. [PMID: 25102080 PMCID: PMC4175982 DOI: 10.1016/j.jmb.2014.07.018] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2014] [Revised: 07/01/2014] [Accepted: 07/20/2014] [Indexed: 12/15/2022]
Abstract
Recently, progress has been made toward understanding the functional diversity of bacterial microcompartment (MCP) systems, which serve as protein-based metabolic organelles in diverse microbes. New types of MCPs have been identified, including the glycyl-radical propanediol (Grp) MCP. Within these elaborate protein complexes, BMC-domain shell proteins [bacterial microcompartment (in reference to the shell protein domain)] assemble to form a polyhedral barrier that encapsulates the enzymatic contents of the MCP. Interestingly, the Grp MCP contains a number of shell proteins with unusual sequence features. GrpU is one such shell protein whose amino acid sequence is particularly divergent from other members of the BMC-domain superfamily of proteins that effectively defines all MCPs. Expression, purification, and subsequent characterization of the protein showed, unexpectedly, that it binds an iron-sulfur cluster. We determined X-ray crystal structures of two GrpU orthologs, providing the first structural insight into the homohexameric BMC-domain shell proteins of the Grp system. The X-ray structures of GrpU, both obtained in the apo form, combined with spectroscopic analyses and computational modeling, show that the metal cluster resides in the central pore of the BMC shell protein at a position of broken 6-fold symmetry. The result is a structurally polymorphic iron-sulfur cluster binding site that appears to be unique among metalloproteins studied to date.
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Affiliation(s)
- Michael C Thompson
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
| | - Nicole M Wheatley
- Molecular Biology Interdepartmental Ph.D. Program, University of California, Los Angeles, CA 90095, USA
| | - Julien Jorda
- University of California, Los Angeles-Department of Energy Institute for Genomics and Proteomics, University of California, Los Angeles, CA 90095, USA
| | - Michael R Sawaya
- University of California, Los Angeles-Department of Energy Institute for Genomics and Proteomics, University of California, Los Angeles, CA 90095, USA
| | - Soheil D Gidaniyan
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
| | - Hoda Ahmed
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
| | - Zhongyu Yang
- Jules Stein Eye Institute, University of California, Los Angeles, CA 90095, USA
| | - Krystal N McCarty
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
| | - Julian P Whitelegge
- Pasarow Mass Spectrometry Laboratory, Neuropsychiatric Institute-Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, CA 90095, USA
| | - Todd O Yeates
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA; University of California, Los Angeles-Department of Energy Institute for Genomics and Proteomics, University of California, Los Angeles, CA 90095, USA; Molecular Biology Institute, University of California, Los Angeles, CA 90095, USA.
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42
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Doi Y, Ikegami Y. Pyruvate formate-lyase is essential for fumarate-independent anaerobic glycerol utilization in the Enterococcus faecalis strain W11. J Bacteriol 2014; 196:2472-80. [PMID: 24769696 PMCID: PMC4054171 DOI: 10.1128/jb.01512-14] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2014] [Accepted: 04/22/2014] [Indexed: 11/20/2022] Open
Abstract
Although anaerobic glycerol metabolism in Enterococcus faecalis requires exogenous fumarate for NADH oxidation, E. faecalis strain W11 can metabolize glycerol in the absence of oxygen without exogenous fumarate. In this study, metabolic end product analyses and reporter assays probing the expression of enzymes involved in pyruvate metabolism were performed to investigate this fumarate-independent anaerobic metabolism of glycerol in W11. Under aerobic conditions, the metabolic end products of W11 cultured with glycerol were similar to those of W11 cultured with glucose. However, when W11 was cultured anaerobically, most of the glucose was converted to l-lactate, but glycerol was converted to ethanol and formate. During anaerobic culture with glycerol, the expression of the l-lactate dehydrogenase and pyruvate dehydrogenase E1αβ genes in W11 was downregulated, whereas the expression of the pyruvate formate-lyase (Pfl) and aldehyde/alcohol dehydrogenase genes was upregulated. These changes in the expression levels caused the change in the composition of end products. A pflB gene disruptant (Δpfl mutant) of W11 could barely utilize glycerol under anaerobic conditions, but the growth of the Δpfl mutant cultured with either glucose or dihydroxyacetone (DHA) under anaerobic conditions was the same as that of W11. Glucose metabolism and DHA generates one NADH molecule per pyruvate molecule, whereas glycerol metabolism in the dehydrogenation pathway generates two NADH molecules per pyruvate molecule. These findings demonstrate that NADH generated from anaerobic glycerol metabolism in the absence of fumarate is oxidized through the Pfl-ethanol fermentation pathway. Thus, Pfl is essential to avoid the accumulation of excess NADH during fumarate-independent anaerobic glycerol metabolism.
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Affiliation(s)
- Yuki Doi
- Department of Applied Chemistry and Biotechnology, Faculty of Engineering, Okayama University of Science, Okayama, Okayama, Japan
| | - Yuki Ikegami
- Department of Applied Chemistry and Biotechnology, Faculty of Engineering, Okayama University of Science, Okayama, Okayama, Japan
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43
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Broderick JB, Duffus B, Duschene KS, Shepard EM. Radical S-adenosylmethionine enzymes. Chem Rev 2014; 114:4229-317. [PMID: 24476342 PMCID: PMC4002137 DOI: 10.1021/cr4004709] [Citation(s) in RCA: 584] [Impact Index Per Article: 58.4] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2013] [Indexed: 12/22/2022]
Affiliation(s)
- Joan B. Broderick
- Department of Chemistry and
Biochemistry, Montana State University, Bozeman, Montana 59717, United States
| | - Benjamin
R. Duffus
- Department of Chemistry and
Biochemistry, Montana State University, Bozeman, Montana 59717, United States
| | - Kaitlin S. Duschene
- Department of Chemistry and
Biochemistry, Montana State University, Bozeman, Montana 59717, United States
| | - Eric M. Shepard
- Department of Chemistry and
Biochemistry, Montana State University, Bozeman, Montana 59717, United States
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44
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Shisler KA, Broderick JB. Glycyl radical activating enzymes: structure, mechanism, and substrate interactions. Arch Biochem Biophys 2014; 546:64-71. [PMID: 24486374 PMCID: PMC4083501 DOI: 10.1016/j.abb.2014.01.020] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2013] [Revised: 01/20/2014] [Accepted: 01/21/2014] [Indexed: 11/20/2022]
Abstract
The glycyl radical enzyme activating enzymes (GRE-AEs) are a group of enzymes that belong to the radical S-adenosylmethionine (SAM) superfamily and utilize a [4Fe-4S] cluster and SAM to catalyze H-atom abstraction from their substrate proteins. GRE-AEs activate homodimeric proteins known as glycyl radical enzymes (GREs) through the production of a glycyl radical. After activation, these GREs catalyze diverse reactions through the production of their own substrate radicals. The GRE-AE pyruvate formate lyase activating enzyme (PFL-AE) is extensively characterized and has provided insights into the active site structure of radical SAM enzymes including GRE-AEs, illustrating the nature of the interactions with their corresponding substrate GREs and external electron donors. This review will highlight research on PFL-AE and will also discuss a few GREs and their respective activating enzymes.
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Affiliation(s)
- Krista A Shisler
- Department of Chemistry & Biochemistry and the Astrobiology Biogeocatalysis Research Center, Montana State University, Bozeman, MT 59717, United States
| | - Joan B Broderick
- Department of Chemistry & Biochemistry and the Astrobiology Biogeocatalysis Research Center, Montana State University, Bozeman, MT 59717, United States.
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45
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Crain AV, Broderick JB. Pyruvate formate-lyase and its activation by pyruvate formate-lyase activating enzyme. J Biol Chem 2013; 289:5723-9. [PMID: 24338017 DOI: 10.1074/jbc.m113.496877] [Citation(s) in RCA: 32] [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
The activation of pyruvate formate-lyase (PFL) by pyruvate formate-lyase activating enzyme (PFL-AE) involves formation of a specific glycyl radical on PFL by the PFL-AE in a reaction requiring S-adenosylmethionine (AdoMet). Surface plasmon resonance experiments were performed under anaerobic conditions on the oxygen-sensitive PFL-AE to determine the kinetics and equilibrium constant for its interaction with PFL. These experiments show that the interaction is very slow and rate-limited by large conformational changes. A novel AdoMet binding assay was used to accurately determine the equilibrium constants for AdoMet binding to PFL-AE alone and in complex with PFL. The PFL-AE bound AdoMet with the same affinity (∼6 μM) regardless of the presence or absence of PFL. Activation of PFL in the presence of its substrate pyruvate or the analog oxamate resulted in stoichiometric conversion of the [4Fe-4S](1+) cluster to the glycyl radical on PFL; however, 3.7-fold less activation was achieved in the absence of these small molecules, demonstrating that pyruvate or oxamate are required for optimal activation. Finally, in vivo concentrations of the entire PFL system were calculated to estimate the amount of bound protein in the cell. PFL, PFL-AE, and AdoMet are essentially fully bound in vivo, whereas electron donor proteins are partially bound.
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Affiliation(s)
- Adam V Crain
- From the Department of Chemistry and Biochemistry and the Astrobiology Biogeocatalysis Research Center, Montana State University, Bozeman, Montana 59717
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46
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Mahoney JK, Martin D, Moore CE, Rheingold AL, Bertrand G. Bottleable (Amino)(Carboxy) Radicals Derived from Cyclic (Alkyl)(Amino) Carbenes. J Am Chem Soc 2013; 135:18766-9. [DOI: 10.1021/ja4104765] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Janell K. Mahoney
- UCSD-CNRS
Joint Research Laboratory (UMI 3555), Department of Chemistry and
Biochemistry, University of California, San Diego, La Jolla, California 92093-0343, United States
| | - David Martin
- UCSD-CNRS
Joint Research Laboratory (UMI 3555), Department of Chemistry and
Biochemistry, University of California, San Diego, La Jolla, California 92093-0343, United States
| | - Curtis E. Moore
- UCSD Crystallography
Facility, San Diego, La Jolla, California 92093-0343, United States
| | - Arnold L. Rheingold
- UCSD Crystallography
Facility, San Diego, La Jolla, California 92093-0343, United States
| | - Guy Bertrand
- UCSD-CNRS
Joint Research Laboratory (UMI 3555), Department of Chemistry and
Biochemistry, University of California, San Diego, La Jolla, California 92093-0343, United States
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47
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Flavodoxin cofactor binding induces structural changes that are required for protein-protein interactions with NADP(+) oxidoreductase and pyruvate formate-lyase activating enzyme. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1834:2512-9. [PMID: 24016774 DOI: 10.1016/j.bbapap.2013.08.014] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2013] [Revised: 08/27/2013] [Accepted: 08/30/2013] [Indexed: 11/23/2022]
Abstract
Flavodoxin (Fld) conformational changes, thermal stability, and cofactor binding were studied using circular dichroism (CD), isothermal titration calorimetry (ITC), and limited proteolysis. Thermodynamics of apo and holo-Fld folding were examined to discern the features of this important electron transfer protein and to provide data on apo-Fld. With the exception of fluorescence and UV-vis binding experiments with its cofactor flavin mononucleotide (FMN), apo-Fld is almost completely uncharacterized in Escherichia coli. Fld is more structured when the FMN cofactor is bound; the association is tight and driven by enthalpy of binding. Surface plasmon resonance binding experiments were carried out under anaerobic conditions for both apo- and holo-Fld and demonstrate the importance of structure and conformation for the interaction with binding partners. Holo-Fld is capable of associating with NADP(+)-dependent flavodoxin oxidoreductase (FNR) and pyruvate formate-lyase activating enzyme (PFL-AE) whereas there is no detectable interaction between apo-Fld and either protein. Limited proteolysis experiments were analyzed by LC-MS to identify the regions in Fld that are involved in conformation changes upon cofactor binding. Docking software was used to model the Fld/PFL-AE complex to understand the interactions between these two proteins and gain insight into electron transfer reactions from Fld to PFL-AE.
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48
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Buckel W. Die bakterielle Methanogenese verläuft radikalisch. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201304593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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49
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Buckel W. Bacterial methanogenesis proceeds by a radical mechanism. Angew Chem Int Ed Engl 2013; 52:8507-9. [PMID: 23852991 DOI: 10.1002/anie.201304593] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2013] [Indexed: 11/09/2022]
Affiliation(s)
- Wolfgang Buckel
- Fachbereich Biologie - Mikrobiologie and Synmikro, Philipps-Universität, 35032 Marburg, Germany.
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50
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The catalytic mechanism for aerobic formation of methane by bacteria. Nature 2013; 497:132-6. [DOI: 10.1038/nature12061] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2012] [Accepted: 03/08/2013] [Indexed: 11/08/2022]
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