1
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Hackmann TJ. The vast landscape of carbohydrate fermentation in prokaryotes. FEMS Microbiol Rev 2024; 48:fuae016. [PMID: 38821505 PMCID: PMC11187502 DOI: 10.1093/femsre/fuae016] [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: 04/05/2024] [Revised: 05/23/2024] [Accepted: 05/29/2024] [Indexed: 06/02/2024] Open
Abstract
Fermentation is a type of metabolism carried out by organisms in environments without oxygen. Despite being studied for over 185 years, the diversity and complexity of this metabolism are just now becoming clear. Our review starts with the definition of fermentation, which has evolved over the years and which we help further refine. We then examine the range of organisms that carry out fermentation and their traits. Over one-fourth of all prokaryotes are fermentative, use more than 40 substrates, and release more than 50 metabolic end products. These insights come from studies analyzing records of thousands of organisms. Next, our review examines the complexity of fermentation at the biochemical level. We map out pathways of glucose fermentation in unprecedented detail, covering over 120 biochemical reactions. We also review recent studies coupling genomics and enzymology to reveal new pathways and enzymes. Our review concludes with practical applications for agriculture, human health, and industry. All these areas depend on fermentation and could be improved through manipulating fermentative microbes and enzymes. We discuss potential approaches for manipulation, including genetic engineering, electrofermentation, probiotics, and enzyme inhibitors. We hope our review underscores the importance of fermentation research and stimulates the next 185 years of study.
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Affiliation(s)
- Timothy J Hackmann
- Department of Animal Science, University of California, Davis, CA 95616, United States
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2
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Kisgeropoulos EC, Artz JH, Blahut M, Peters JW, King PW, Mulder DW. Properties of the iron-sulfur cluster electron transfer relay in an [FeFe]-hydrogenase that is tuned for H 2 oxidation catalysis. J Biol Chem 2024; 300:107292. [PMID: 38636659 PMCID: PMC11126806 DOI: 10.1016/j.jbc.2024.107292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Revised: 04/09/2024] [Accepted: 04/11/2024] [Indexed: 04/20/2024] Open
Abstract
[FeFe]-hydrogenases catalyze the reversible oxidation of H2 from electrons and protons at an organometallic active site cofactor named the H-cluster. In addition to the H-cluster, most [FeFe]-hydrogenases possess accessory FeS cluster (F-cluster) relays that function in mediating electron transfer with catalysis. There is significant variation in the structural properties of F-cluster relays among the [FeFe]-hydrogenases; however, it is unknown how this variation relates to the electronic and thermodynamic properties, and thus the electron transfer properties, of enzymes. Clostridium pasteurianum [FeFe]-hydrogenase II (CpII) exhibits a large catalytic bias for H2 oxidation (compared to H2 production), making it a notable system for examining if F-cluster properties contribute to the overall function and efficiency of the enzyme. By applying a combination of multifrequency and potentiometric electron paramagnetic resonance, we resolved two electron paramagnetic resonance signals with distinct power- and temperature-dependent properties at g = 2.058 1.931 1.891 (F2.058) and g = 2.061 1.920 1.887 (F2.061), with assigned midpoint potentials of -140 ± 18 mV and -406 ± 12 mV versus normal hydrogen electrode, respectively. Spectral analysis revealed features consistent with spin-spin coupling between the two [4Fe-4S] F-clusters, and possible functional models are discussed that account for the contribution of coupling to the electron transfer landscape. The results signify the interplay of electronic coupling and free energy properties and parameters of the FeS clusters to the electron transfer mechanism through the relay and provide new insight as to how relays functionally complement the catalytic directionality of active sites to achieve highly efficient catalysis.
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Affiliation(s)
| | - Jacob H Artz
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado, USA
| | - Matthew Blahut
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado, USA
| | - John W Peters
- Department of Chemistry and Biochemistry, The University of Oklahoma, Norman, Oklahoma, USA
| | - Paul W King
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado, USA; Renewable and Sustainable Energy Institute, National Renewable Energy Laboratory and University of Colorado Boulder, Boulder, Colorado, USA
| | - David W Mulder
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado, USA.
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3
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Feng X, Schut GJ, Adams MWW, Li H. Structures and Electron Transport Paths in the Four Families of Flavin-Based Electron Bifurcation Enzymes. Subcell Biochem 2024; 104:383-408. [PMID: 38963493 DOI: 10.1007/978-3-031-58843-3_14] [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: 07/05/2024]
Abstract
Oxidoreductases facilitating electron transfer between molecules are pivotal in metabolic pathways. Flavin-based electron bifurcation (FBEB), a recently discovered energy coupling mechanism in oxidoreductases, enables the reversible division of electron pairs into two acceptors, bridging exergonic and otherwise unfeasible endergonic reactions. This chapter explores the four distinct FBEB complex families and highlights a decade of structural insights into FBEB complexes. In this chapter, we discuss the architecture, electron transfer routes, and conformational changes across all FBEB families, revealing the structural foundation that facilitate these remarkable functions.
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Affiliation(s)
- Xiang Feng
- Division of Chemistry and Chemical Engineering, Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA, USA
| | - Gerrit J Schut
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA
| | - Michael W W Adams
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA
| | - Huilin Li
- Department of Structural Biology, Van Andel Institute, Grand Rapids, MI, USA.
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4
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Ge X, Schut GJ, Tran J, Poole II FL, Niks D, Menjivar K, Hille R, Adams MWW. Characterization of the Membrane-Associated Electron-Bifurcating Flavoenzyme EtfABCX from the Hyperthermophilic Bacterium Thermotoga maritima. Biochemistry 2023; 62:3554-3567. [PMID: 38061393 PMCID: PMC10734219 DOI: 10.1021/acs.biochem.3c00473] [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: 09/05/2023] [Revised: 11/20/2023] [Accepted: 11/20/2023] [Indexed: 12/20/2023]
Abstract
Electron bifurcation is an energy-conservation mechanism in which a single enzyme couples an exergonic reaction with an endergonic one. Heterotetrameric EtfABCX drives the reduction of low-potential ferredoxin (E°' ∼ -450 mV) by oxidation of the midpotential NADH (E°' = -320 mV) by simultaneously coupling the reaction to reduction of the high-potential menaquinone (E°' = -74 mV). Electron bifurcation occurs at the NADH-oxidizing bifurcating-flavin adenine dinucleotide (BF-FAD) in EtfA, which has extremely crossed half-potentials and passes the first, high-potential electron to an electron-transferring FAD and via two iron-sulfur clusters eventually to menaquinone. The low-potential electron on the BF-FAD semiquinone simultaneously reduces ferredoxin. We have expressed the genes encodingThermotoga maritimaEtfABCX in E. coli and purified the EtfABCX holoenzyme and the EtfAB subcomplex. The bifurcation activity of EtfABCX was demonstrated by using electron paramagnetic resonance (EPR) to follow accumulation of reduced ferredoxin. To elucidate structural factors that impart the bifurcating ability, EPR and NADH titrations monitored by visible spectroscopy and dye-linked enzyme assays have been employed to characterize four conserved residues, R38, P239, and V242 in EtfA and R140 in EtfB, in the immediate vicinity of the BF-FAD. The R38, P239, and V242 variants showed diminished but still significant bifurcation activity. Despite still being partially reduced by NADH, the R140 variant had no bifurcation activity, and electron transfer to its two [4Fe-4S] clusters was prevented. The role of R140 is discussed in terms of the bifurcation mechanism in EtfABCX and in the other three families of bifurcating enzymes.
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Affiliation(s)
- Xiaoxuan Ge
- Department
of Biochemistry and Molecular Biology, University
of Georgia, Athens, Georgia 30602, United States
| | - Gerrit J. Schut
- Department
of Biochemistry and Molecular Biology, University
of Georgia, Athens, Georgia 30602, United States
| | - Jessica Tran
- Department
of Biochemistry, University of California,
Riverside, Riverside, California 92507, United States
| | - Farris L. Poole II
- Department
of Biochemistry and Molecular Biology, University
of Georgia, Athens, Georgia 30602, United States
| | - Dimitri Niks
- Department
of Biochemistry, University of California,
Riverside, Riverside, California 92507, United States
| | - Kevin Menjivar
- Department
of Biochemistry, University of California,
Riverside, Riverside, California 92507, United States
| | - Russ Hille
- Department
of Biochemistry, University of California,
Riverside, Riverside, California 92507, United States
| | - Michael W. W. Adams
- Department
of Biochemistry and Molecular Biology, University
of Georgia, Athens, Georgia 30602, United States
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5
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Ortiz S, Niks D, Wiley S, Lubner CE, Hille R. Rapid-reaction kinetics of the bifurcating NAD +-dependent NADPH:ferredoxin oxidoreductase NfnI from Pyrococcus furiosus. J Biol Chem 2023; 299:105403. [PMID: 38229399 PMCID: PMC10724689 DOI: 10.1016/j.jbc.2023.105403] [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: 07/12/2023] [Revised: 10/02/2023] [Accepted: 10/22/2023] [Indexed: 01/18/2024] Open
Abstract
We have investigated the kinetics of NAD+-dependent NADPH:ferredoxin oxidoreductase (NfnI), a bifurcating transhydrogenase that takes two electron pairs from NADPH to reduce two ferredoxins and one NAD+ through successive bifurcation events. NADPH reduction takes place at the bifurcating FAD of NfnI's large subunit, with high-potential electrons transferred to the [2Fe-2S] cluster and S-FADH of the small subunit, ultimately on to NAD+; low-potential electrons are transferred to two [4Fe-4S] clusters of the large subunit and on to ferredoxin. Reduction of NfnI by NADPH goes to completion only at higher pH, with a limiting kred of 36 ± 1.6 s-1 and apparent KdNADPH of 5 ± 1.2 μM. Reduction of one of the [4Fe-4S] clusters of NfnI occurs within a second, indicating that in the absence of NAD+, the system can bifurcate and generate low-potential electrons without NAD+. When enzyme is reduced by NADPH in the absence of NAD+ but the presence of ferredoxin, up to three equivalents of ferredoxin become reduced, although the reaction is considerably slower than seen during steady-state turnover. Bifurcation appears to be limited by transfer of the first, high-potential electron into the high-potential pathway. Ferredoxin reduction without NAD+ demonstrates that electron bifurcation is an intrinsic property of the bifurcating FAD and is not dependent on the simultaneous presence of NAD+ and ferredoxin. The tight coupling between NAD+ and ferredoxin reduction observed under multiple-turnover conditions is instead simply due to the need to remove reducing equivalents from the high-potential electron pathway under multiple-turnover conditions.
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Affiliation(s)
- Steve Ortiz
- Department of Biochemistry and the Biophysics Graduate Program, University of California, Riverside, USA
| | - Dimitri Niks
- Department of Biochemistry and the Biophysics Graduate Program, University of California, Riverside, USA
| | - Seth Wiley
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado, USA
| | - Carolyn E Lubner
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado, USA.
| | - Russ Hille
- Department of Biochemistry and the Biophysics Graduate Program, University of California, Riverside, USA.
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6
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Kumar A, Kremp F, Roth J, Freibert SA, Müller V, Schuller JM. Molecular architecture and electron transfer pathway of the Stn family transhydrogenase. Nat Commun 2023; 14:5484. [PMID: 37673911 PMCID: PMC10482914 DOI: 10.1038/s41467-023-41212-x] [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: 03/21/2023] [Accepted: 08/27/2023] [Indexed: 09/08/2023] Open
Abstract
The challenge of endergonic reduction of NADP+ using NADH is overcome by ferredoxin-dependent transhydrogenases that employ electron bifurcation for electron carrier adjustments in the ancient Wood-Ljungdahl pathway. Recently, an electron-bifurcating transhydrogenase with subunit compositions distinct from the well-characterized Nfn-type transhydrogenase was described: the Stn complex. Here, we present the single-particle cryo-EM structure of the Stn family transhydrogenase from the acetogenic bacterium Sporomusa ovata and functionally dissect its electron transfer pathway. Stn forms a tetramer consisting of functional heterotrimeric StnABC complexes. Our findings demonstrate that the StnAB subunits assume the structural and functional role of a bifurcating module, homologous to the HydBC core of the electron-bifurcating HydABC complex. Moreover, StnC contains a NuoG-like domain and a GltD-like NADPH binding domain that resembles the NfnB subunit of the NfnAB complex. However, in contrast to NfnB, StnC lost the ability to bifurcate electrons. Structural comparison allows us to describe how the same fold on one hand evolved bifurcation activity on its own while on the other hand combined with an associated bifurcating module, exemplifying modular evolution in anaerobic metabolism to produce activities critical for survival at the thermodynamic limit of life.
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Affiliation(s)
- Anuj Kumar
- SYNMIKRO Research Center and Department of Chemistry, Philipps-University of Marburg, Marburg, Germany
- Department of Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Frankfurt am Main, Germany
| | - Florian Kremp
- Department of Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Frankfurt am Main, Germany
| | - Jennifer Roth
- Department of Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Frankfurt am Main, Germany
| | - Sven A Freibert
- SYNMIKRO Research Center and Department of Chemistry, Philipps-University of Marburg, Marburg, Germany
- Institut für Zytobiologie im Zentrum SYNMIKRO, Philipps-University of Marburg, Marburg, Germany
- Core Facility "Protein Biochemistry and Spectroscopy", Marburg, 35032, Germany
| | - Volker Müller
- Department of Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Frankfurt am Main, Germany.
| | - Jan M Schuller
- SYNMIKRO Research Center and Department of Chemistry, Philipps-University of Marburg, Marburg, Germany.
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7
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Ortiz S, Niks D, Vigil W, Tran J, Lubner CE, Hille R. Spectral deconvolution of electron-bifurcating flavoproteins. Methods Enzymol 2023; 685:531-550. [PMID: 37245914 DOI: 10.1016/bs.mie.2023.03.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Electron-bifurcating flavoproteins catalyze the tightly coupled reduction of high- and low-potential acceptors using a median-potential electron donor, and are invariably complex systems with multiple redox-active centers in two or more subunits. Methods are described that permit, in favorable cases, the deconvolution of spectral changes associated with reduction of specific centers, making it possible to dissect the overall process of electron bifurcation into individual, discrete steps.
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Affiliation(s)
- Steve Ortiz
- Department of Biochemistry, University of California, Riverside, United States
| | - Dimitri Niks
- Department of Biochemistry, University of California, Riverside, United States
| | - Wayne Vigil
- Department of Biochemistry, University of California, Riverside, United States
| | - Jessica Tran
- Department of Biochemistry, University of California, Riverside, United States
| | - Carolyn E Lubner
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, United States.
| | - Russ Hille
- Department of Biochemistry, University of California, Riverside, United States.
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8
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Kronen M, Vázquez-Campos X, Wilkins MR, Lee M, Manefield MJ. Evidence for a Putative Isoprene Reductase in Acetobacterium wieringae. mSystems 2023; 8:e0011923. [PMID: 36943133 PMCID: PMC10134865 DOI: 10.1128/msystems.00119-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2023] Open
Abstract
Recent discoveries of isoprene-metabolizing microorganisms suggest they might play an important role in the global isoprene budget. Under anoxic conditions, isoprene can be used as an electron acceptor and is reduced to methylbutene. This study describes the proteogenomic profiling of an isoprene-reducing bacterial culture to identify organisms and genes responsible for the isoprene hydrogenation reaction. A metagenome-assembled genome (MAG) of the most abundant (89% relative abundance) lineage in the enrichment, Acetobacterium wieringae, was obtained. Comparative proteogenomics and reverse transcription-PCR (RT-PCR) identified a putative five-gene operon from the A. wieringae MAG upregulated during isoprene reduction. The operon encodes a putative oxidoreductase, three pleiotropic nickel chaperones (2 × HypA, HypB), and one 4Fe-4S ferredoxin. The oxidoreductase is proposed as the putative isoprene reductase with a binding site for NADH, flavin adenine dinucleotide (FAD), two pairs of canonical [4Fe-4S] clusters, and a putative iron-sulfur cluster site in a Cys6-bonding environment. Well-studied Acetobacterium strains, such as A. woodii DSM 1030, A. wieringae DSM 1911, or A. malicum DSM 4132, do not encode the isoprene-regulated operon but encode, like many other bacteria, a homolog of the putative isoprene reductase (~47 to 49% amino acid sequence identity). Uncharacterized homologs of the putative isoprene reductase are observed across the Firmicutes, Spirochaetes, Tenericutes, Actinobacteria, Chloroflexi, Bacteroidetes, and Proteobacteria, suggesting the ability of biohydrogenation of unfunctionalized conjugated doubled bonds in other unsaturated hydrocarbons. IMPORTANCE Isoprene was recently shown to act as an electron acceptor for a homoacetogenic bacterium. The focus of this study is the molecular basis for isoprene reduction. By comparing a genome from our isoprene-reducing enrichment culture, dominated by Acetobacterium wieringae, with genomes of other Acetobacterium lineages that do not reduce isoprene, we shortlisted candidate genes for isoprene reduction. Using comparative proteogenomics and reverse transcription-PCR we have identified a putative five-gene operon encoding an oxidoreductase referred to as putative isoprene reductase.
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Affiliation(s)
- Miriam Kronen
- UNSW Water Research Centre, School of Civil and Environmental Engineering, University of New South Wales, Sydney, NSW, Australia
| | - Xabier Vázquez-Campos
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Marc R Wilkins
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Matthew Lee
- UNSW Water Research Centre, School of Civil and Environmental Engineering, University of New South Wales, Sydney, NSW, Australia
| | - Michael J Manefield
- UNSW Water Research Centre, School of Civil and Environmental Engineering, University of New South Wales, Sydney, NSW, Australia
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9
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Katsyv A, Kumar A, Saura P, Pöverlein MC, Freibert SA, T Stripp S, Jain S, Gamiz-Hernandez AP, Kaila VRI, Müller V, Schuller JM. Molecular Basis of the Electron Bifurcation Mechanism in the [FeFe]-Hydrogenase Complex HydABC. J Am Chem Soc 2023; 145:5696-5709. [PMID: 36811855 PMCID: PMC10021017 DOI: 10.1021/jacs.2c11683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
Abstract
Electron bifurcation is a fundamental energy coupling mechanism widespread in microorganisms that thrive under anoxic conditions. These organisms employ hydrogen to reduce CO2, but the molecular mechanisms have remained enigmatic. The key enzyme responsible for powering these thermodynamically challenging reactions is the electron-bifurcating [FeFe]-hydrogenase HydABC that reduces low-potential ferredoxins (Fd) by oxidizing hydrogen gas (H2). By combining single-particle cryo-electron microscopy (cryoEM) under catalytic turnover conditions with site-directed mutagenesis experiments, functional studies, infrared spectroscopy, and molecular simulations, we show that HydABC from the acetogenic bacteria Acetobacterium woodii and Thermoanaerobacter kivui employ a single flavin mononucleotide (FMN) cofactor to establish electron transfer pathways to the NAD(P)+ and Fd reduction sites by a mechanism that is fundamentally different from classical flavin-based electron bifurcation enzymes. By modulation of the NAD(P)+ binding affinity via reduction of a nearby iron-sulfur cluster, HydABC switches between the exergonic NAD(P)+ reduction and endergonic Fd reduction modes. Our combined findings suggest that the conformational dynamics establish a redox-driven kinetic gate that prevents the backflow of the electrons from the Fd reduction branch toward the FMN site, providing a basis for understanding general mechanistic principles of electron-bifurcating hydrogenases.
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Affiliation(s)
- Alexander Katsyv
- Department of Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Frankfurt am Main 60438, Germany
| | - Anuj Kumar
- Department of Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Frankfurt am Main 60438, Germany.,SYNMIKRO Research Center and Department of Chemistry, Philipps-University of Marburg, Marburg 35032, Germany
| | - Patricia Saura
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm 10691, Sweden
| | - Maximilian C Pöverlein
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm 10691, Sweden
| | - Sven A Freibert
- Institut für Zytobiologie im Zentrum SYNMIKRO, Philipps-University of Marburg, Marburg 35032, Germany.,Core Facility "Protein Biochemistry and Spectroscopy", Marburg 35032, Germany
| | - Sven T Stripp
- Department of Physics, Experimental Molecular Biophysics, Freie Universität Berlin, Berlin 14195, Germany
| | - Surbhi Jain
- Department of Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Frankfurt am Main 60438, Germany
| | - Ana P Gamiz-Hernandez
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm 10691, Sweden
| | - Ville R I Kaila
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm 10691, Sweden
| | - Volker Müller
- Department of Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Frankfurt am Main 60438, Germany
| | - Jan M Schuller
- SYNMIKRO Research Center and Department of Chemistry, Philipps-University of Marburg, Marburg 35032, Germany
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10
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Evolving a New Electron Transfer Pathway for Nitrogen Fixation Uncovers an Electron Bifurcating-Like Enzyme Involved in Anaerobic Aromatic Compound Degradation. mBio 2023; 14:e0288122. [PMID: 36645294 PMCID: PMC9973337 DOI: 10.1128/mbio.02881-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Nitrogenase is the key enzyme involved in nitrogen fixation and uses low potential electrons delivered by ferredoxin (Fd) or flavodoxin (Fld) to reduce dinitrogen gas (N2) to produce ammonia, generating hydrogen gas (H2) as an obligate product of this activity. Although the phototrophic alphaproteobacterium Rhodopseudomonas palustris encodes multiple proteins that can reduce Fd, the FixABCX complex is the only one shown to support nitrogen fixation, and R. palustris Fix- mutants grow poorly under nitrogen-fixing conditions. To investigate how native electron transfer chains (ETCs) can be redirected toward nitrogen fixation, we leveraged the strong selective pressure of nitrogen limitation to isolate a suppressor of an R. palustris ΔfixC strain that grows under nitrogen-fixing conditions. We found two mutations were required to restore growth under nitrogen-fixing conditions in the absence of functional FixABCX. One mutation was in the gene encoding the primary Fd involved in nitrogen fixation, fer1, and the other mutation was in aadN, which encodes a homolog of NAD+-dependent Fd:NADPH oxidoreductase (Nfn). We present evidence that AadN plays a role in electron transfer to benzoyl coenzyme A reductase, the key enzyme involved in anaerobic aromatic compound degradation. Our data support a model where the ETC for anaerobic aromatic compound degradation was repurposed to support nitrogen fixation in the ΔfixC suppressor strain. IMPORTANCE There is increasing evidence that protein electron carriers like Fd evolved to form specific partnerships with select electron donors and acceptors to keep native electron transfer pathways insulated from one another. This makes it challenging to integrate a Fd-dependent pathway such as biological nitrogen fixation into non-nitrogen-fixing organisms and provide the high-energy reducing power needed to fix nitrogen. Here, we show that amino acid substitutions in an electron donor for anaerobic aromatic compound degradation and an Fd involved in nitrogen fixation enabled electron transfer to nitrogenase. This study provides a model system to understand electron transfer chain specificity and how new electron transfer pathways can be evolved for biotechnologically valuable pathways like nitrogen fixation.
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11
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Huynh TN, Stewart V. Purine catabolism by enterobacteria. Adv Microb Physiol 2023; 82:205-266. [PMID: 36948655 DOI: 10.1016/bs.ampbs.2023.01.001] [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: 02/13/2023]
Abstract
Purines are abundant among organic nitrogen sources and have high nitrogen content. Accordingly, microorganisms have evolved different pathways to catabolize purines and their metabolic products such as allantoin. Enterobacteria from the genera Escherichia, Klebsiella and Salmonella have three such pathways. First, the HPX pathway, found in the genus Klebsiella and very close relatives, catabolizes purines during aerobic growth, extracting all four nitrogen atoms in the process. This pathway includes several known or predicted enzymes not previously observed in other purine catabolic pathways. Second, the ALL pathway, found in strains from all three species, catabolizes allantoin during anaerobic growth in a branched pathway that also includes glyoxylate assimilation. This allantoin fermentation pathway originally was characterized in a gram-positive bacterium, and therefore is widespread. Third, the XDH pathway, found in strains from Escherichia and Klebsiella spp., at present is ill-defined but likely includes enzymes to catabolize purines during anaerobic growth. Critically, this pathway may include an enzyme system for anaerobic urate catabolism, a phenomenon not previously described. Documenting such a pathway would overturn the long-held assumption that urate catabolism requires oxygen. Overall, this broad capability for purine catabolism during either aerobic or anaerobic growth suggests that purines and their metabolites contribute to enterobacterial fitness in a variety of environments.
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Affiliation(s)
- TuAnh Ngoc Huynh
- Department of Food Science, University of Wisconsin, Madison, WI, United States
| | - Valley Stewart
- Department of Microbiology & Molecular Genetics, University of California, Davis, CA, United States.
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12
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Chakraborty S, Bhattacharjee S, Tiwari B, Jaishwal T, Singh SS, Mishra AK. Deciphering the mechanisms of zinc tolerance in the cyanobacterium Anabaena sphaerica and its zinc bioremediation potential. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:9591-9608. [PMID: 36057058 DOI: 10.1007/s11356-022-22388-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 07/29/2022] [Indexed: 06/15/2023]
Abstract
Cyanobacteria adopt a variety of changes at proteomic and metabolic levels for surviving under harmful environmental conditions including heavy metal stress. The current study investigates the impact of zinc stress on the proteome of Anabaena sphaerica to get an insight into its molecular mechanisms of zinc tolerance. The study revealed three different aspects that were associated with the zinc tolerance in A. sphaerica: (i) the reduced expression of photosynthesis, nitrogen fixation, energy metabolism, respiratory, and transcriptional/translational proteins probably to conserve energy and utilizing it to sustain growth; (ii) the enhanced expression of metallothionein and ferritin domain protein All 3940 to chelate free zinc ions whereas upregulation of antioxidative proteins for detoxifying reactive oxygen species; and (iii) the expression of large numbers of hypothetical proteins to maintain the important cellular functions. Furthermore, over expressions of sulfate adenylyl transferase and cystathionine beta synthase along with the increased synthesis of peptidases and thiolated antioxidant proteins were also noticed which denoted cysteine synthesis under sulfur deprivation possibly by mobilizing the sulfur from dead cells and its channelization towards the production of thiolated antioxidants. Besides tolerating excess amount of zinc, A. sphaerica exhibited high zinc biosorption efficiency which confirmed its outstanding zinc bioremediation potential.
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Affiliation(s)
- Sindhunath Chakraborty
- Laboratory of Microbial Genetics, Department of Botany, Banaras Hindu University, Varanasi, 221005, India
| | - Samujjal Bhattacharjee
- Laboratory of Microbial Genetics, Department of Botany, Banaras Hindu University, Varanasi, 221005, India
| | - Balkrishna Tiwari
- Laboratory of Microbial Genetics, Department of Botany, Banaras Hindu University, Varanasi, 221005, India
| | - Tameshwar Jaishwal
- Laboratory of Microbial Genetics, Department of Botany, Banaras Hindu University, Varanasi, 221005, India
- Laboratory of Cyanobacterial Systematics and Stress Biology, Department of Botany, Banaras Hindu University, Varanasi, 221005, India
| | - Satya Shila Singh
- Laboratory of Cyanobacterial Systematics and Stress Biology, Department of Botany, Banaras Hindu University, Varanasi, 221005, India
| | - Arun Kumar Mishra
- Laboratory of Microbial Genetics, Department of Botany, Banaras Hindu University, Varanasi, 221005, India.
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13
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Noori MT, Min B. Fundamentals and recent progress in bioelectrochemical system-assisted biohythane production. BIORESOURCE TECHNOLOGY 2022; 361:127641. [PMID: 35863600 DOI: 10.1016/j.biortech.2022.127641] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 07/13/2022] [Accepted: 07/14/2022] [Indexed: 06/15/2023]
Abstract
Biohythane, a balanced mixture of 10%-30% v/v of hydrogen and 70%-90% v/v of methane, could be the backbone of an all-purpose future energy supply. Recently, bioelectrochemical systems (BES) became a new sensation among environmental biotechnology processes with the potential to sustainably generate biohythane. Therefore, to unleash its full potential for scaling up, researchers are consistently improving microbial metabolic pathways, novel reactors, and electrode designs. This review presents a detailed analysis of recently discovered fundamental mechanisms and science and engineering intervention of different strategies to improve the biohythane composition and production rate from BES. However, several milestones are to be achieved, for instance, improving electrode kinetics using efficient catalysts, engineered microbial communities, and improved reactor configurations, for commercializing this sustainable technology. Thus, a future perspective section is included to recommend novel research lines, mainly focusing on the microbial communities and the efficient electrocatalysts, to enhance reactor performance.
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Affiliation(s)
- Md Tabish Noori
- Department of Environmental Science and Engineering, Kyung Hee University - Global Campus, Yongin-Si, Republic of Korea
| | - Booki Min
- Department of Environmental Science and Engineering, Kyung Hee University - Global Campus, Yongin-Si, Republic of Korea.
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14
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Site-Differentiated Iron–Sulfur Cluster Ligation Affects Flavin-Based Electron Bifurcation Activity. Metabolites 2022; 12:metabo12090823. [PMID: 36144227 PMCID: PMC9503767 DOI: 10.3390/metabo12090823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 08/25/2022] [Accepted: 08/28/2022] [Indexed: 11/16/2022] Open
Abstract
Electron bifurcation is an elegant mechanism of biological energy conversion that effectively couples three different physiologically relevant substrates. As such, enzymes that perform this function often play critical roles in modulating cellular redox metabolism. One such enzyme is NADH-dependent reduced-ferredoxin: NADP+ oxidoreductase (NfnSL), which couples the thermodynamically favorable reduction of NAD+ to drive the unfavorable reduction of ferredoxin from NADPH. The interaction of NfnSL with its substrates is constrained to strict stoichiometric conditions, which ensures minimal energy losses from non-productive intramolecular electron transfer reactions. However, the determinants for this are not well understood. One curious feature of NfnSL is that both initial acceptors of bifurcated electrons are unique iron–sulfur (FeS) clusters containing one non-cysteinyl ligand each. The biochemical impact and mechanistic roles of site-differentiated FeS ligands are enigmatic, despite their incidence in many redox active enzymes. Herein, we describe the biochemical study of wild-type NfnSL and a variant in which one of the site-differentiated ligands has been replaced with a cysteine. Results of dye-based steady-state kinetics experiments, substrate-binding measurements, biochemical activity assays, and assessments of electron distribution across the enzyme indicate that this site-differentiated ligand in NfnSL plays a role in maintaining fidelity of the coordinated reactions performed by the two electron transfer pathways. Given the commonality of these cofactors, our findings have broad implications beyond electron bifurcation and mechanistic biochemistry and may inform on means of modulating the redox balance of the cell for targeted metabolic engineering approaches.
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15
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Liang J, Huang H, Wang Y, Li L, Yi J, Wang S. A Cytoplasmic NAD(P)H-Dependent Polysulfide Reductase with Thiosulfate Reductase Activity from the Hyperthermophilic Bacterium Thermotoga maritima. Microbiol Spectr 2022; 10:e0043622. [PMID: 35762779 PMCID: PMC9431562 DOI: 10.1128/spectrum.00436-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 06/05/2022] [Indexed: 11/22/2022] Open
Abstract
Thermotoga maritima is an anaerobic hyperthermophilic bacterium that efficiently produces H2 by fermenting carbohydrates. High concentration of H2 inhibits the growth of T. maritima, and S0 could eliminate the inhibition and stimulate the growth through its reduction. The mechanism of T. maritima sulfur reduction, however, has not been fully understood. Herein, based on its similarity with archaeal NAD(P)H-dependent sulfur reductases (NSR), the ORF THEMA_RS02810 was identified and expressed in Escherichia coli, and the recombinant protein was characterized. The purified flavoprotein possessed NAD(P)H-dependent S0 reductase activity (1.3 U/mg for NADH and 0.8 U/mg for NADPH), polysulfide reductase activity (0.32 U/mg for NADH and 0.35 U/mg for NADPH), and thiosulfate reductase activity (2.3 U/mg for NADH and 2.5 U/mg for NADPH), which increased 3~4-folds by coenzyme A stimulation. Quantitative RT-PCR analysis showed that nsr was upregulated together with the mbx, yeeE, and rnf genes when the strain grew in S0- or thiosulfate-containing medium. The mechanism for sulfur reduction in T. maritima was discussed, which may affect the redox balance and energy metabolism of T. maritima. Genome search revealed that NSR homolog is widely distributed in thermophilic bacteria and archaea, implying its important role in the sulfur cycle of geothermal environments. IMPORTANCE The reduction of S0 and thiosulfate is essential in the sulfur cycle of geothermal environments, in which thermophiles play an important role. Despite previous research on some sulfur reductases of thermophilic archaea, the mechanism of sulfur reduction in thermophilic bacteria is still not clearly understood. Herein, we confirmed the presence of a cytoplasmic NAD(P)H-dependent polysulfide reductase (NSR) from the hyperthermophile T. maritima, with S0, polysulfide, and thiosulfate reduction activities, in contrast to other sulfur reductases. When grown in S0- or thiosulfate-containing medium, its expression was upregulated. And the putative membrane-bound MBX and Rnf may also play a role in the metabolism, which might influence the redox balance and energy metabolism of T. maritima. This is distinct from the mechanism of sulfur reduction in mesophiles such as Wolinella succinogenes. NSR homologs are widely distributed among heterotrophic thermophiles, suggesting that they may be vital in the sulfur cycle in geothermal environments.
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Affiliation(s)
- Jiyu Liang
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, People’s Republic of China
| | - Haiyan Huang
- Department of Pathogen Biology, School of Basic Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, People’s Republic of China
| | - Yubo Wang
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, People’s Republic of China
| | - Lexin Li
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, People’s Republic of China
| | - Jihong Yi
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, People’s Republic of China
| | - Shuning Wang
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, People’s Republic of China
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16
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Schut GJ, Haja DK, Feng X, Poole FL, Li H, Adams MWW. An Abundant and Diverse New Family of Electron Bifurcating Enzymes With a Non-canonical Catalytic Mechanism. Front Microbiol 2022; 13:946711. [PMID: 35875533 PMCID: PMC9304861 DOI: 10.3389/fmicb.2022.946711] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 06/15/2022] [Indexed: 11/13/2022] Open
Abstract
Microorganisms utilize electron bifurcating enzymes in metabolic pathways to carry out thermodynamically unfavorable reactions. Bifurcating FeFe-hydrogenases (HydABC) reversibly oxidize NADH (E′∼−280 mV, under physiological conditions) and reduce protons to H2 gas (E°′−414 mV) by coupling this endergonic reaction to the exergonic reduction of protons by reduced ferredoxin (Fd) (E′∼−500 mV). We show here that HydABC homologs are surprisingly ubiquitous in the microbial world and are represented by 57 phylogenetically distinct clades but only about half are FeFe-hydrogenases. The others have replaced the hydrogenase domain with another oxidoreductase domain or they contain additional subunits, both of which enable various third reactions to be reversibly coupled to NAD+ and Fd reduction. We hypothesize that all of these enzymes carry out electron bifurcation and that their third substrates can include hydrogen peroxide, pyruvate, carbon monoxide, aldehydes, aryl-CoA thioesters, NADP+, cofactor F420, formate, and quinones, as well as many yet to be discovered. Some of the enzymes are proposed to be integral membrane-bound proton-translocating complexes. These different functionalities are associated with phylogenetically distinct clades and in many cases with specific microbial phyla. We propose that this new and abundant class of electron bifurcating enzyme be referred to as the Bfu family whose defining feature is a conserved bifurcating BfuBC core. This core contains FMN and six iron sulfur clusters and it interacts directly with ferredoxin (Fd) and NAD(H). Electrons to or from the third substrate are fed into the BfuBC core via BfuA. The other three known families of electron bifurcating enzyme (abbreviated as Nfn, EtfAB, and HdrA) contain a special FAD that bifurcates electrons to high and low potential pathways. The Bfu family are proposed to use a different electron bifurcation mechanism that involves a combination of FMN and three adjacent iron sulfur clusters, including a novel [2Fe-2S] cluster with pentacoordinate and partial non-Cys coordination. The absolute conservation of the redox cofactors of BfuBC in all members of the Bfu enzyme family indicate they have the same non-canonical mechanism to bifurcate electrons. A hypothetical catalytic mechanism is proposed as a basis for future spectroscopic analyses of Bfu family members.
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Affiliation(s)
- Gerrit J. Schut
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, United States
| | - Dominik K. Haja
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, United States
| | - Xiang Feng
- Department of Structural Biology, Van Andel Institute, Grand Rapids, MI, United States
| | - Farris L. Poole
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, United States
| | - Huilin Li
- Department of Structural Biology, Van Andel Institute, Grand Rapids, MI, United States
| | - Michael W. W. Adams
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, United States
- *Correspondence: Michael W. W. Adams, ; orcid.org/0000-0002-9796-5014
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17
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Kayastha K, Katsyv A, Himmrich C, Welsch S, Schuller JM, Ermler U, Müller V. Structure-based electron-confurcation mechanism of the Ldh-EtfAB complex. eLife 2022; 11:77095. [PMID: 35748623 PMCID: PMC9232219 DOI: 10.7554/elife.77095] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 05/22/2022] [Indexed: 01/22/2023] Open
Abstract
Lactate oxidation with NAD+ as electron acceptor is a highly endergonic reaction. Some anaerobic bacteria overcome the energetic hurdle by flavin-based electron bifurcation/confurcation (FBEB/FBEC) using a lactate dehydrogenase (Ldh) in concert with the electron-transferring proteins EtfA and EtfB. The electron cryo-microscopically characterized (Ldh-EtfAB)2 complex of Acetobacterium woodii at 2.43 Å resolution consists of a mobile EtfAB shuttle domain located between the rigid central Ldh and the peripheral EtfAB base units. The FADs of Ldh and the EtfAB shuttle domain contact each other thereby forming the D (dehydrogenation-connected) state. The intermediary Glu37 and Glu139 may harmonize the redox potentials between the FADs and the pyruvate/lactate pair crucial for FBEC. By integrating Alphafold2 calculations a plausible novel B (bifurcation-connected) state was obtained allowing electron transfer between the EtfAB base and shuttle FADs. Kinetic analysis of enzyme variants suggests a correlation between NAD+ binding site and D-to-B-state transition implicating a 75° rotation of the EtfAB shuttle domain. The FBEC inactivity when truncating the ferredoxin domain of EtfA substantiates its role as redox relay. Lactate oxidation in Ldh is assisted by the catalytic base His423 and a metal center. On this basis, a comprehensive catalytic mechanism of the FBEC process was proposed.
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Affiliation(s)
- Kanwal Kayastha
- Departments of Molecular Membrane Biology of the Max-Planck-Institut for Biophysics, Frankfurt am Main, Germany
| | - Alexander Katsyv
- Department of Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Goethe University, Frankfurt am Main, Germany
| | - Christina Himmrich
- Department of Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Goethe University, Frankfurt am Main, Germany
| | - Sonja Welsch
- Central Electron Microscopy Facility, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Jan M Schuller
- SYNMICRO Research Center and Department of Chemistry, Philipps University, Marburg, Germany
| | - Ulrich Ermler
- Departments of Molecular Membrane Biology of the Max-Planck-Institut for Biophysics, Frankfurt am Main, Germany
| | - Volker Müller
- Department of Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Goethe University, Frankfurt am Main, Germany
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18
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Lubner CE, Artz JH, Mulder DW, Oza A, Ward RJ, Williams SG, Jones AK, Peters JW, Smalyukh II, Bharadwaj VS, King PW. A site-differentiated [4Fe-4S] cluster controls electron transfer reactivity of Clostridium acetobutylicum [FeFe]-hydrogenase I. Chem Sci 2022; 13:4581-4588. [PMID: 35656134 PMCID: PMC9019909 DOI: 10.1039/d1sc07120c] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 03/24/2022] [Indexed: 01/11/2023] Open
Abstract
One of the many functions of reduction–oxidation (redox) cofactors is to mediate electron transfer in biological enzymes catalyzing redox-based chemical transformation reactions. There are numerous examples of enzymes that utilize redox cofactors to form electron transfer relays to connect catalytic sites to external electron donors and acceptors. The compositions of relays are diverse and tune transfer thermodynamics and kinetics towards the chemical reactivity of the enzyme. Diversity in relay design is exemplified among different members of hydrogenases, enzymes which catalyze reversible H2 activation, which also couple to diverse types of donor and acceptor molecules. The [FeFe]-hydrogenase I from Clostridium acetobutylicum (CaI) is a member of a large family of structurally related enzymes where interfacial electron transfer is mediated by a terminal, non-canonical, His-coordinated, [4Fe–4S] cluster. The function of His coordination was examined by comparing the biophysical properties and reactivity to a Cys substituted variant of CaI. This demonstrated that His coordination strongly affected the distal [4Fe–4S] cluster spin state, spin pairing, and spatial orientations of molecular orbitals, with a minor effect on reduction potential. The deviations in these properties by substituting His for Cys in CaI, correlated with pronounced changes in electron transfer and reactivity with the native electron donor–acceptor ferredoxin. The results demonstrate that differential coordination of the surface localized [4Fe–4S]His cluster in CaI is utilized to control intermolecular and intramolecular electron transfer where His coordination creates a physical and electronic environment that enables facile electron exchange between electron carrier molecules and the iron–sulfur cluster relay for coupling to reversible H2 activation at the catalytic site. Histidine coordination of the distal [4Fe–4S] cluster in [FeFe]-hydrogenase was demonstrated to tune the cluster spin-states, spin-pairing and surrounding molecular orbitals to enable more facile electron transfer compared to cysteine coordination.![]()
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Affiliation(s)
| | - Jacob H Artz
- National Renewable Energy Laboratory Golden Colorado USA
| | - David W Mulder
- National Renewable Energy Laboratory Golden Colorado USA
| | - Aisha Oza
- National Renewable Energy Laboratory Golden Colorado USA
| | - Rachel J Ward
- Department of Physics, University of Colorado Boulder Boulder Colorado USA
| | - S Garrett Williams
- School of Molecular Sciences, Arizona State University Tempe Arizona USA.,Sandia National Laboratories Albuquerque New Mexico USA
| | - Anne K Jones
- School of Molecular Sciences, Arizona State University Tempe Arizona USA
| | - John W Peters
- Institute of Biological Chemistry, Washington State University Pullman Washington USA
| | - Ivan I Smalyukh
- Department of Physics, University of Colorado Boulder Boulder Colorado USA.,Renewable and Sustainable Energy Institute, National Renewable Energy Laboratory and University of Colorado Boulder Boulder Colorado USA
| | | | - Paul W King
- National Renewable Energy Laboratory Golden Colorado USA .,Renewable and Sustainable Energy Institute, National Renewable Energy Laboratory and University of Colorado Boulder Boulder Colorado USA
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19
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Chen SC, Ji J, Popp D, Jaekel U, Richnow HH, Sievert SM, Musat F. Genome and proteome analyses show the gaseous alkane degrader Desulfosarcina sp. strain BuS5 as an extreme metabolic specialist. Environ Microbiol 2022; 24:1964-1976. [PMID: 35257474 DOI: 10.1111/1462-2920.15956] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 02/23/2022] [Indexed: 11/30/2022]
Abstract
The metabolic potential of the sulfate-reducing bacterium Desulfosarcina sp. strain BuS5, currently the only pure culture able to oxidize the volatile alkanes propane and butane without oxygen, was investigated via genomics, proteomics and physiology assays. Complete genome sequencing revealed that strain BuS5 encodes a single alkyl-succinate synthase, an enzyme which apparently initiates oxidation of both propane and butane. The formed alkyl-succinates are oxidized to CO2 via beta oxidation and the oxidative Wood-Ljungdahl pathways as shown by proteogenomics analyses. Strain BuS5 conserves energy via the canonical sulfate reduction pathway and electron bifurcation. An ability to utilize long-chain fatty acids, mannose and oligopeptides, suggested by automated annotation pipelines, was not supported by physiology assays and in-depth analyses of the corresponding genetic systems. Consistently, comparative genomics revealed a streamlined BuS5 genome with a remarkable paucity of catabolic modules. These results establish strain BuS5 as an exceptional metabolic specialist, able to grow only with propane and butane, for which we propose the name Desulfosarcina aeriophaga BuS5. This highly restrictive lifestyle, most likely the result of habitat-driven evolutionary gene loss, may provide D. aeriophaga BuS5 a competitive edge in sediments impacted by natural gas seeps. Etymology: Desulfosarcina aeriophaga, aério (Greek): gas; phágos (Greek): eater; D. aeriophaga: a gas eating or gas feeding Desulfosarcina.
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Affiliation(s)
- Song-Can Chen
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Jiaheng Ji
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Denny Popp
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | | | - Hans-Hermann Richnow
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Stefan M Sievert
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA, 02543, USA
| | - Florin Musat
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany.,Department of Molecular Biology and Biotechnology, Faculty of Biology and Geology, Babeş-Bolyai University, Cluj-Napoca, Romania
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20
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Understanding flavin electronic structure and spectra. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2022. [DOI: 10.1002/wcms.1541] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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21
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Crystallographic snapshots of a B 12-dependent radical SAM methyltransferase. Nature 2022; 602:336-342. [PMID: 35110733 PMCID: PMC8828468 DOI: 10.1038/s41586-021-04355-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 12/15/2021] [Indexed: 01/01/2023]
Abstract
By catalysing the microbial formation of methane, methyl-coenzyme M reductase has a central role in the global levels of this greenhouse gas1,2. The activity of methyl-coenzyme M reductase is profoundly affected by several unique post-translational modifications3–6, such as a unique C-methylation reaction catalysed by methanogenesis marker protein 10 (Mmp10), a radical S-adenosyl-l-methionine (SAM) enzyme7,8. Here we report the spectroscopic investigation and atomic resolution structure of Mmp10 from Methanosarcina acetivorans, a unique B12 (cobalamin)-dependent radical SAM enzyme9. The structure of Mmp10 reveals a unique enzyme architecture with four metallic centres and critical structural features involved in the control of catalysis. In addition, the structure of the enzyme–substrate complex offers a glimpse into a B12-dependent radical SAM enzyme in a precatalytic state. By combining electron paramagnetic resonance spectroscopy, structural biology and biochemistry, our study illuminates the mechanism by which the emerging superfamily of B12-dependent radical SAM enzymes catalyse chemically challenging alkylation reactions and identifies distinctive active site rearrangements to provide a structural rationale for the dual use of the SAM cofactor for radical and nucleophilic chemistry. Structural and spectroscopic studies show how a B12-dependent radical SAM enzyme catalyses unique and challenging alkylation chemistry, including protein post-translational modification required for methane biosynthesis.
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22
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Chadwick GL, Skennerton CT, Laso-Pérez R, Leu AO, Speth DR, Yu H, Morgan-Lang C, Hatzenpichler R, Goudeau D, Malmstrom R, Brazelton WJ, Woyke T, Hallam SJ, Tyson GW, Wegener G, Boetius A, Orphan VJ. Comparative genomics reveals electron transfer and syntrophic mechanisms differentiating methanotrophic and methanogenic archaea. PLoS Biol 2022; 20:e3001508. [PMID: 34986141 PMCID: PMC9012536 DOI: 10.1371/journal.pbio.3001508] [Citation(s) in RCA: 49] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 04/15/2022] [Accepted: 12/08/2021] [Indexed: 11/25/2022] Open
Abstract
The anaerobic oxidation of methane coupled to sulfate reduction is a microbially mediated process requiring a syntrophic partnership between anaerobic methanotrophic (ANME) archaea and sulfate-reducing bacteria (SRB). Based on genome taxonomy, ANME lineages are polyphyletic within the phylum Halobacterota, none of which have been isolated in pure culture. Here, we reconstruct 28 ANME genomes from environmental metagenomes and flow sorted syntrophic consortia. Together with a reanalysis of previously published datasets, these genomes enable a comparative analysis of all marine ANME clades. We review the genomic features that separate ANME from their methanogenic relatives and identify what differentiates ANME clades. Large multiheme cytochromes and bioenergetic complexes predicted to be involved in novel electron bifurcation reactions are well distributed and conserved in the ANME archaea, while significant variations in the anabolic C1 pathways exists between clades. Our analysis raises the possibility that methylotrophic methanogenesis may have evolved from a methanotrophic ancestor. A comparative genomics study of anaerobic methanotrophic (ANME) archaea reveals the genetic "parts list" associated with the repeated evolutionary transition between methanogenic and methanotrophic metabolism in the archaeal domain of life.
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Affiliation(s)
- Grayson L. Chadwick
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, California, United States of America
- * E-mail: (GLC); (VJO)
| | - Connor T. Skennerton
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, California, United States of America
| | - Rafael Laso-Pérez
- Max-Planck Institute for Marine Microbiology, Bremen, Germany
- MARUM, Center for Marine Environmental Science, and Department of Geosciences, University of Bremen, Bremen, Germany
| | - Andy O. Leu
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, Australia
| | - Daan R. Speth
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, California, United States of America
| | - Hang Yu
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, California, United States of America
| | - Connor Morgan-Lang
- Graduate Program in Bioinformatics, University of British Columbia, Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Roland Hatzenpichler
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, California, United States of America
| | - Danielle Goudeau
- US Department of Energy Joint Genome Institute, Berkeley, California, United States of America
| | - Rex Malmstrom
- US Department of Energy Joint Genome Institute, Berkeley, California, United States of America
| | - William J. Brazelton
- School of Biological Sciences, University of Utah, Salt Lake City, Utah, United States of America
| | - Tanja Woyke
- US Department of Energy Joint Genome Institute, Berkeley, California, United States of America
| | - Steven J. Hallam
- Graduate Program in Bioinformatics, University of British Columbia, Genome Sciences Centre, Vancouver, British Columbia, Canada
- Department of Microbiology & Immunology, University of British Columbia, British Columbia, Canada
- Genome Science and Technology Program, University of British Columbia, Vancouver, British Columbia, Canada
- ECOSCOPE Training Program, University of British Columbia, Vancouver, British Columbia, Canada
- Life Sciences Institute, University of British Columbia, British Columbia, Canada
| | - Gene W. Tyson
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, Australia
| | - Gunter Wegener
- Max-Planck Institute for Marine Microbiology, Bremen, Germany
- MARUM, Center for Marine Environmental Science, and Department of Geosciences, University of Bremen, Bremen, Germany
| | - Antje Boetius
- Max-Planck Institute for Marine Microbiology, Bremen, Germany
- MARUM, Center for Marine Environmental Science, and Department of Geosciences, University of Bremen, Bremen, Germany
- Alfred Wegener Institute, Helmholtz Center for Polar and Marine Research, Bremerhaven, Germany
| | - Victoria J. Orphan
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, California, United States of America
- * E-mail: (GLC); (VJO)
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23
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Moalic Y, Hartunians J, Dalmasso C, Courtine D, Georges M, Oger P, Shao Z, Jebbar M, Alain K. The Piezo-Hyperthermophilic Archaeon Thermococcus piezophilus Regulates Its Energy Efficiency System to Cope With Large Hydrostatic Pressure Variations. Front Microbiol 2021; 12:730231. [PMID: 34803948 PMCID: PMC8595942 DOI: 10.3389/fmicb.2021.730231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 10/13/2021] [Indexed: 11/23/2022] Open
Abstract
Deep-sea ecosystems share a common physical parameter, namely high hydrostatic pressure (HHP). Some of the microorganisms isolated at great depths have a high physiological plasticity to face pressure variations. The adaptive strategies by which deep-sea microorganisms cope with HHP variations remain to be elucidated, especially considering the extent of their biotopes on Earth. Herein, we investigated the gene expression patterns of Thermococcus piezophilus, a piezohyperthermophilic archaeon isolated from the deepest hydrothermal vent known to date, under sub-optimal, optimal and supra-optimal pressures (0.1, 50, and 90 MPa, respectively). At stressful pressures [sub-optimal (0.1 MPa) and supra-optimal (90 MPa) conditions], no classical stress response was observed. Instead, we observed an unexpected transcriptional modulation of more than a hundred gene clusters, under the putative control of the master transcriptional regulator SurR, some of which are described as being involved in energy metabolism. This suggests a fine-tuning effect of HHP on the SurR regulon. Pressure could act on gene regulation, in addition to modulating their expression.
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Affiliation(s)
- Yann Moalic
- Univ Brest, CNRS, Ifremer, Laboratoire de Microbiologie des Environnements Extrêmes LM2E, UMR 6197, IUEM, Plouzané, France.,IRP 1211 MicrobSea, Sino-French Laboratory of Deep-Sea Microbiology, LM2E, Plouzané, France
| | - Jordan Hartunians
- Univ Brest, CNRS, Ifremer, Laboratoire de Microbiologie des Environnements Extrêmes LM2E, UMR 6197, IUEM, Plouzané, France.,IRP 1211 MicrobSea, Sino-French Laboratory of Deep-Sea Microbiology, LM2E, Plouzané, France
| | - Cécile Dalmasso
- Univ Brest, CNRS, Ifremer, Laboratoire de Microbiologie des Environnements Extrêmes LM2E, UMR 6197, IUEM, Plouzané, France.,IRP 1211 MicrobSea, Sino-French Laboratory of Deep-Sea Microbiology, LM2E, Plouzané, France
| | - Damien Courtine
- Univ Brest, CNRS, Ifremer, Laboratoire de Microbiologie des Environnements Extrêmes LM2E, UMR 6197, IUEM, Plouzané, France.,IRP 1211 MicrobSea, Sino-French Laboratory of Deep-Sea Microbiology, LM2E, Plouzané, France
| | - Myriam Georges
- Univ Brest, CNRS, Ifremer, Laboratoire de Microbiologie des Environnements Extrêmes LM2E, UMR 6197, IUEM, Plouzané, France.,IRP 1211 MicrobSea, Sino-French Laboratory of Deep-Sea Microbiology, LM2E, Plouzané, France
| | - Philippe Oger
- Université de Lyon, INSA Lyon, CNRS UMR 5240, Villeurbanne, France
| | - Zongze Shao
- IRP 1211 MicrobSea, Sino-French Laboratory of Deep-Sea Microbiology, LM2E, Plouzané, France.,Key Laboratory of Marine Biogenetic Resources, The Third Institute of Oceanography SOA, Xiamen, China
| | - Mohamed Jebbar
- Univ Brest, CNRS, Ifremer, Laboratoire de Microbiologie des Environnements Extrêmes LM2E, UMR 6197, IUEM, Plouzané, France.,IRP 1211 MicrobSea, Sino-French Laboratory of Deep-Sea Microbiology, LM2E, Plouzané, France
| | - Karine Alain
- Univ Brest, CNRS, Ifremer, Laboratoire de Microbiologie des Environnements Extrêmes LM2E, UMR 6197, IUEM, Plouzané, France.,IRP 1211 MicrobSea, Sino-French Laboratory of Deep-Sea Microbiology, LM2E, Plouzané, France
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24
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Song Z, Wei C, Li C, Gao X, Mao S, Lu F, Qin HM. Customized exogenous ferredoxin functions as an efficient electron carrier. BIORESOUR BIOPROCESS 2021; 8:109. [PMID: 38650207 PMCID: PMC10992505 DOI: 10.1186/s40643-021-00464-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 10/28/2021] [Indexed: 11/10/2022] Open
Abstract
Ferredoxin (Fdx) is regarded as the main electron carrier in biological electron transfer and acts as an electron donor in metabolic pathways of many organisms. Here, we screened a self-sufficient P450-derived reductase PRF with promising production yield of 9OHAD (9α-hydroxy4-androstene-3,17-dione) from AD, and further proved the importance of [2Fe-2S] clusters of ferredoxin-oxidoreductase in transferring electrons in steroidal conversion. The results of truncated Fdx domain in all oxidoreductases and mutagenesis data elucidated the indispensable role of [2Fe-2S] clusters in the electron transfer process. By adding the independent plant-type Fdx to the reaction system, the AD (4-androstene-3,17-dione) conversion rate have been significantly improved. A novel efficient electron transfer pathway of PRF + Fdx + KshA (KshA, Rieske-type oxygenase of 3-ketosteroid-9-hydroxylase) in the reaction system rather than KshAB complex system was proposed based on analysis of protein-protein interactions and redox potential measurement. Adding free Fdx created a new conduit for electrons to travel from reductase to oxygenase. This electron transfer pathway provides new insight for the development of efficient exogenous Fdx as an electron carrier.
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Affiliation(s)
- Zhan Song
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin University of Science and Technology, Tianjin, 300457, People's Republic of China
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, People's Republic of China
- National Engineering Laboratory for Industrial Enzymes, Tianjin University of Science and Technology, Tianjin, 300457, People's Republic of China
| | - Cancan Wei
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin University of Science and Technology, Tianjin, 300457, People's Republic of China
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, People's Republic of China
- National Engineering Laboratory for Industrial Enzymes, Tianjin University of Science and Technology, Tianjin, 300457, People's Republic of China
| | - Chao Li
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin University of Science and Technology, Tianjin, 300457, People's Republic of China
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, People's Republic of China
- National Engineering Laboratory for Industrial Enzymes, Tianjin University of Science and Technology, Tianjin, 300457, People's Republic of China
| | - Xin Gao
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin University of Science and Technology, Tianjin, 300457, People's Republic of China
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, People's Republic of China
- National Engineering Laboratory for Industrial Enzymes, Tianjin University of Science and Technology, Tianjin, 300457, People's Republic of China
| | - Shuhong Mao
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin University of Science and Technology, Tianjin, 300457, People's Republic of China.
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, People's Republic of China.
- National Engineering Laboratory for Industrial Enzymes, Tianjin University of Science and Technology, Tianjin, 300457, People's Republic of China.
| | - Fuping Lu
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin University of Science and Technology, Tianjin, 300457, People's Republic of China.
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, People's Republic of China.
- National Engineering Laboratory for Industrial Enzymes, Tianjin University of Science and Technology, Tianjin, 300457, People's Republic of China.
| | - Hui-Min Qin
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin University of Science and Technology, Tianjin, 300457, People's Republic of China.
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, People's Republic of China.
- National Engineering Laboratory for Industrial Enzymes, Tianjin University of Science and Technology, Tianjin, 300457, People's Republic of China.
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25
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Buckel W. Energy Conservation in Fermentations of Anaerobic Bacteria. Front Microbiol 2021; 12:703525. [PMID: 34589068 PMCID: PMC8473912 DOI: 10.3389/fmicb.2021.703525] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 07/30/2021] [Indexed: 02/04/2023] Open
Abstract
Anaerobic bacteria ferment carbohydrates and amino acids to obtain energy for growth. Due to the absence of oxygen and other inorganic electron acceptors, the substrate of a fermentation has to serve as electron donor as well as acceptor, which results in low free energies as compared to that of aerobic oxidations. Until about 10 years ago, anaerobes were thought to exclusively use substrate level phosphorylation (SLP), by which only part of the available energy could be conserved. Therefore, anaerobes were regarded as unproductive and inefficient energy conservers. The discovery of electrochemical Na+ gradients generated by biotin-dependent decarboxylations or by reduction of NAD+ with ferredoxin changed this view. Reduced ferredoxin is provided by oxidative decarboxylation of 2-oxoacids and the recently discovered flavin based electron bifurcation (FBEB). In this review, the two different fermentation pathways of glutamate to ammonia, CO2, acetate, butyrate and H2 via 3-methylaspartate or via 2-hydroxyglutarate by members of the Firmicutes are discussed as prototypical examples in which all processes characteristic for fermentations occur. Though the fermentations proceed on two entirely different pathways, the maximum theoretical amount of ATP is conserved in each pathway. The occurrence of the 3-methylaspartate pathway in clostridia from soil and the 2-hydroxyglutarate pathway in the human microbiome of the large intestine is traced back to the oxygen-sensitivity of the radical enzymes. The coenzyme B12-dependent glutamate mutase in the 3-methylaspartate pathway tolerates oxygen, whereas 2-hydroxyglutaryl-CoA dehydratase is extremely oxygen-sensitive and can only survive in the gut, where the combustion of butyrate produced by the microbiome consumes the oxygen and provides a strict anaerobic environment. Examples of coenzyme B12-dependent eliminases are given, which in the gut are replaced by simpler extremely oxygen sensitive glycyl radical enzymes.
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Affiliation(s)
- Wolfgang Buckel
- Laboratorium für Mikrobiologie, Fachbereich Biologie, Philipps-Universität Marburg, Marburg, Germany
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26
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Yuly JL, Zhang P, Ru X, Terai K, Singh N, Beratan DN. Efficient and reversible electron bifurcation with either normal or inverted potentials at the bifurcating cofactor. Chem 2021. [DOI: 10.1016/j.chempr.2021.03.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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27
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Debabov VG. Acetogens: Biochemistry, Bioenergetics, Genetics, and Biotechnological Potential. Microbiology (Reading) 2021. [DOI: 10.1134/s0026261721030024] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
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28
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Vanoni MA. Iron-sulfur flavoenzymes: the added value of making the most ancient redox cofactors and the versatile flavins work together. Open Biol 2021; 11:210010. [PMID: 33947244 PMCID: PMC8097209 DOI: 10.1098/rsob.210010] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Iron-sulfur (Fe-S) flavoproteins form a broad and growing class of complex, multi-domain and often multi-subunit proteins coupling the most ancient cofactors (the Fe-S clusters) and the most versatile coenzymes (the flavin coenzymes, FMN and FAD). These enzymes catalyse oxidoreduction reactions usually acting as switches between donors of electron pairs and acceptors of single electrons, and vice versa. Through selected examples, the enzymes' structure−function relationships with respect to rate and directionality of the electron transfer steps, the role of the apoprotein and its dynamics in modulating the electron transfer process will be discussed.
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Affiliation(s)
- Maria Antonietta Vanoni
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133 Milano, Italy
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29
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Kayastha K, Vitt S, Buckel W, Ermler U. Flavins in the electron bifurcation process. Arch Biochem Biophys 2021; 701:108796. [PMID: 33609536 DOI: 10.1016/j.abb.2021.108796] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 02/01/2021] [Accepted: 02/03/2021] [Indexed: 11/18/2022]
Abstract
The discovery of a new energy-coupling mechanism termed flavin-based electron bifurcation (FBEB) in 2008 revealed a novel field of application for flavins in biology. The key component is the bifurcating flavin endowed with strongly inverted one-electron reduction potentials (FAD/FAD•- ≪ FAD•-/FADH-) that cooperatively transfers in its reduced state one low and one high-energy electron into different directions and thereby drives an endergonic with an exergonic reduction reaction. As energy splitting at the bifurcating flavin apparently implicates one-electron chemistry, the FBEB machinery has to incorporate prior to and behind the central bifurcating flavin 2e-to-1e and 1e-to-2e switches, frequently also flavins, for oxidizing variable medium-potential two-electron donating substrates and for reducing high-potential two-electron accepting substrates. The one-electron carriers ferredoxin or flavodoxin serve as low-potential (high-energy) electron acceptors, which power endergonic processes almost exclusively in obligate anaerobic microorganisms to increase the efficiency of their energy metabolism. In this review, we outline the global organization of FBEB enzymes, the functions of the flavins therein and the surrounding of the isoalloxazine rings by which their reduction potentials are specifically adjusted in a finely tuned energy landscape.
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Affiliation(s)
- Kanwal Kayastha
- Max-Planck-Institut für Biophysik, Max-von-Laue-Str. 3, 60438, Frankfurt am Main, Germany
| | - Stella Vitt
- Max-Planck-Institut für Biophysik, Max-von-Laue-Str. 3, 60438, Frankfurt am Main, Germany; Laboratorium für Mikrobiologie, Fachbereich Biologie and SYNMIKRO, Philipps-Universität, 35032, Marburg, Germany
| | - Wolfgang Buckel
- Laboratorium für Mikrobiologie, Fachbereich Biologie and SYNMIKRO, Philipps-Universität, 35032, Marburg, Germany; Max-Planck-Institut für terrestrische Mikrobiologie, Karl-von-Frisch-Str. 10, 35043, Marburg, Germany
| | - Ulrich Ermler
- Max-Planck-Institut für Biophysik, Max-von-Laue-Str. 3, 60438, Frankfurt am Main, Germany.
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30
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Appel L, Willistein M, Dahl C, Ermler U, Boll M. Functional diversity of prokaryotic HdrA(BC) modules: Role in flavin-based electron bifurcation processes and beyond. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2021; 1862:148379. [PMID: 33460586 DOI: 10.1016/j.bbabio.2021.148379] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 01/08/2021] [Accepted: 01/11/2021] [Indexed: 10/22/2022]
Abstract
In methanogenic archaea, the archetypical complex of heterodisulfide reductase (HdrABC) and hydrogenase (MvhAGD) couples the endergonic reduction of CO2 by H2 to the exergonic reduction of the CoB-S-S-CoM heterodisulfide by H2 via flavin-based electron bifurcation. Presently known enzymes containing HdrA(BC)-like components play key roles in methanogenesis, acetogenesis, respiratory sulfate reduction, lithotrophic reduced sulfur compound oxidation, aromatic compound degradation, fermentations, and probably many further processes. This functional diversity is achieved by a modular architecture of HdrA(BC) enzymes, where a big variety of electron input/output modules may be connected either directly or via adaptor modules to the HdrA(BC) components. Many, but not all HdrA(BC) complexes are proposed to catalyse a flavin-based electron bifurcation/confurcation. Despite the availability of HdrA(BC) crystal structures, fundamental questions of electron transfer and energy coupling processes remain. Here, we address the common properties and functional diversity of HdrA(BC) core modules integrated into electron-transfer machineries of outstanding complexity.
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Affiliation(s)
- Lena Appel
- Fakultät für Biologie - Mikrobiologie, Universität Freiburg, Freiburg, Germany
| | - Max Willistein
- Fakultät für Biologie - Mikrobiologie, Universität Freiburg, Freiburg, Germany
| | - Christiane Dahl
- Institut für Mikrobiologie & Biotechnologie, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | - Ulrich Ermler
- Max-Planck-Institut für Biophysik, Frankfurt, Germany
| | - Matthias Boll
- Fakultät für Biologie - Mikrobiologie, Universität Freiburg, Freiburg, Germany.
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31
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Wise CE, Ledinina AE, Yuly JL, Artz JH, Lubner CE. The role of thermodynamic features on the functional activity of electron bifurcating enzymes. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2021; 1862:148377. [PMID: 33453185 DOI: 10.1016/j.bbabio.2021.148377] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 01/05/2021] [Accepted: 01/06/2021] [Indexed: 11/25/2022]
Abstract
Electron bifurcation is a biological mechanism to drive a thermodynamically unfavorable redox reaction through direct coupling with an exergonic reaction. This process allows microorganisms to generate high energy reducing equivalents in order to sustain life and is often found in anaerobic metabolism, where the energy economy of the cell is poor. Recent work has revealed details of the redox energy landscapes for a variety of electron bifurcating enzymes, greatly expanding the understanding of how energy is transformed by this unique mechanism. Here we highlight the plasticity of these emerging landscapes, what is known regarding their mechanistic underpinnings, and provide a context for interpreting their biochemical activity within the physiological framework. We conclude with an outlook for propelling the field toward an integrative understanding of the impact of electron bifurcation.
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Affiliation(s)
| | | | | | - Jacob H Artz
- National Renewable Energy Laboratory, Golden, CO, USA
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32
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Löffler M, Wallerang KB, Venceslau SS, Pereira IAC, Dahl C. The Iron-Sulfur Flavoprotein DsrL as NAD(P)H:Acceptor Oxidoreductase in Oxidative and Reductive Dissimilatory Sulfur Metabolism. Front Microbiol 2020; 11:578209. [PMID: 33178160 PMCID: PMC7596348 DOI: 10.3389/fmicb.2020.578209] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 09/23/2020] [Indexed: 11/13/2022] Open
Abstract
DsrAB-type dissimilatory sulfite reductase is a key enzyme of microbial sulfur-dependent energy metabolism. Sulfur oxidizers also contain DsrL, which is essential for sulfur oxidation in Allochromatium vinosum. This NAD(P)H oxidoreductase acts as physiological partner of oxidative-type rDsrAB. Recent analyses uncovered that DsrL is not confined to sulfur oxidizers but also occurs in (probable) sulfate/sulfur-reducing bacteria. Here, phylogenetic analysis revealed a separation into two major branches, DsrL-1, with two subgroups, and DsrL-2. When present in organisms with reductive-type DsrAB, DsrL is of type 2. In the majority of cases oxidative-type rDsrAB occurs with DsrL-1 but combination with DsrL-2-type enzymes is also observed. Three model DsrL proteins, DsrL-1A and DsrL-1B from the sulfur oxidizers A. vinosum and Chlorobaculum tepidum, respectively, as well as DsrL-2 from thiosulfate- and sulfur-reducing Desulfurella amilsii were kinetically characterized. DaDsrL-2 is active with NADP(H) but not with NAD(H) which we relate to a conserved YRR-motif in the substrate-binding domains of all DsrL-2 enzymes. In contrast, AvDsrL-1A has a strong preference for NAD(H) and the CtDsrL-1B enzyme is completely inactive with NADP(H). Thus, NAD+ as well as NADP+ are suitable in vivo electron acceptors for rDsrABL-1-catalyzed sulfur oxidation, while NADPH is required as electron donor for sulfite reduction. This observation can be related to the lower redox potential of the NADPH/NADP+ than the NADH/NAD+ couple under physiological conditions. Organisms with a rdsrAB and dsrL-1 gene combination can be confidently identified as sulfur oxidizers while predictions for organisms with other combinations require much more caution and additional information sources.
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Affiliation(s)
- Maria Löffler
- Institut für Mikrobiologie & Biotechnologie, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | - Kai B Wallerang
- Institut für Mikrobiologie & Biotechnologie, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | - Sofia S Venceslau
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Inês A C Pereira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Christiane Dahl
- Institut für Mikrobiologie & Biotechnologie, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
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33
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Kremp F, Roth J, Müller V. The Sporomusa type Nfn is a novel type of electron-bifurcating transhydrogenase that links the redox pools in acetogenic bacteria. Sci Rep 2020; 10:14872. [PMID: 32913242 PMCID: PMC7483475 DOI: 10.1038/s41598-020-71038-2] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 08/07/2020] [Indexed: 11/15/2022] Open
Abstract
Flavin-based electron bifurcation is a long hidden mechanism of energetic coupling present mainly in anaerobic bacteria and archaea that suffer from energy limitations in their environment. Electron bifurcation saves precious cellular ATP and enables lithotrophic life of acetate-forming (acetogenic) bacteria that grow on H2 + CO2 by the only pathway that combines CO2 fixation with ATP synthesis, the Wood–Ljungdahl pathway. The energy barrier for the endergonic reduction of NADP+, an electron carrier in the Wood–Ljungdahl pathway, with NADH as reductant is overcome by an electron-bifurcating, ferredoxin-dependent transhydrogenase (Nfn) but many acetogens lack nfn genes. We have purified a ferredoxin-dependent NADH:NADP+ oxidoreductase from Sporomusa ovata, characterized the enzyme biochemically and identified the encoding genes. These studies led to the identification of a novel, Sporomusa type Nfn (Stn), built from existing modules of enzymes such as the soluble [Fe–Fe] hydrogenase, that is widespread in acetogens and other anaerobic bacteria.
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Affiliation(s)
- Florian Kremp
- Department of Molecular Microbiology and Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Max-von-Laue Str. 9, 60438, Frankfurt, Germany
| | - Jennifer Roth
- Department of Molecular Microbiology and Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Max-von-Laue Str. 9, 60438, Frankfurt, Germany
| | - Volker Müller
- Department of Molecular Microbiology and Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Max-von-Laue Str. 9, 60438, Frankfurt, Germany.
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34
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The Rnf complex is a Na + coupled respiratory enzyme in a fermenting bacterium, Thermotoga maritima. Commun Biol 2020; 3:431. [PMID: 32770029 PMCID: PMC7414866 DOI: 10.1038/s42003-020-01158-y] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 07/15/2020] [Indexed: 11/21/2022] Open
Abstract
rnf genes are widespread in bacteria and biochemical and genetic data are in line with the hypothesis that they encode a membrane-bound enzyme that oxidizes reduced ferredoxin and reduces NAD and vice versa, coupled to ion transport across the cytoplasmic membrane. The Rnf complex is of critical importance in many bacteria for energy conservation but also for reverse electron transport to drive ferredoxin reduction. However, the enzyme has never been purified and thus, ion transport could not be demonstrated yet. Here, we have purified the Rnf complex from the anaerobic, fermenting thermophilic bacterium Thermotoga maritima and show that is a primary Na+ pump. These studies provide the proof that the Rnf complex is indeed an ion (Na+) translocating, respiratory enzyme. Together with a Na+-F1FO ATP synthase it builds a simple, two-limb respiratory chain in T. maritima. The physiological role of electron transport phosphorylation in a fermenting bacterium is discussed. From a fermenting bacterium, Thermotoga maritima, Kuhns, Trifunovi ć et al. purify a complex that includes a respiratory enzyme, Rnf. They find that the Rnf complex requires Na+ for activity and that it catalyzes Na+ transport in liposomes. This study shows that the Rnf complex is indeed an ion translocating, respiratory enzyme.
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35
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Ethanol Metabolism Dynamics in Clostridium ljungdahlii Grown on Carbon Monoxide. Appl Environ Microbiol 2020; 86:AEM.00730-20. [PMID: 32414802 DOI: 10.1128/aem.00730-20] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 05/11/2020] [Indexed: 01/10/2023] Open
Abstract
Bioethanol production from syngas using acetogenic bacteria has attracted considerable attention in recent years. However, low ethanol yield is the biggest challenge that prevents the commercialization of syngas fermentation into biofuels using microbial catalysts. The present study demonstrated that ethanol metabolism plays an important role in recycling NADH/NAD+ during autotrophic growth. Deletion of bifunctional aldehyde/alcohol dehydrogenase (adhE) genes leads to significant growth deficiencies in gas fermentation. Using specific fermentation technology in which the gas pressure and pH were constantly controlled at 0.1 MPa and 6.0, respectively, we revealed that ethanol was formed during the exponential phase, closely accompanied by biomass production. Then, ethanol was oxidized to acetate via the aldehyde ferredoxin oxidoreductase pathway in Clostridium ljungdahlii A metabolic experiment using 13C-labeled ethanol and acetate, redox balance analysis, and comparative transcriptomic analysis demonstrated that ethanol production and reuse shared the metabolic pathway but occurred at different growth phases.IMPORTANCE Ethanol production from carbon monoxide (CO) as a carbon and energy source by Clostridium ljungdahlii and "Clostridium autoethanogenum" is currently being commercialized. During gas fermentation, ethanol synthesis is NADH-dependent. However, ethanol oxidation and its regulatory mechanism remain incompletely understood. Energy metabolism analysis demonstrated that reduced ferredoxin is the sole source of NADH formation by the Rnf-ATPase system, which provides ATP for cell growth during CO fermentation. Therefore, ethanol production is tightly linked to biomass production (ATP production). Clarification of the mechanism of ethanol oxidation and biosynthesis can provide an important reference for generating high-ethanol-yield strains of C. ljungdahlii in the future.
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36
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Zhu HF, Liu ZY, Zhou X, Yi JH, Lun ZM, Wang SN, Tang WZ, Li FL. Energy Conservation and Carbon Flux Distribution During Fermentation of CO or H 2/CO 2 by Clostridium ljungdahlii. Front Microbiol 2020; 11:416. [PMID: 32256473 PMCID: PMC7092622 DOI: 10.3389/fmicb.2020.00416] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 02/27/2020] [Indexed: 11/23/2022] Open
Abstract
Both CO and H2 can be utilized as energy sources during the autotrophic growth of Clostridium ljungdahlii. In principle, CO is a more energetically and thermodynamically favorable energy source for gas fermentation in comparison to H2. Therefore, metabolism may vary during growth under different energy sources. In this study, C. ljungdahlii was fed with CO and/or CO2/H2 at pH 6.0 with a gas pressure of 0.1 MPa. C. ljungdahlii primarily produced acetate in the presence of H2 as an energy source, but produced alcohols with CO as an energy source under the same fermentation conditions. A key enzyme activity assay, metabolic flux analysis, and comparative transcriptomics were performed for investigating the response mechanism of C. ljungdahlii under different energy sources. A CO dehydrogenase and an aldehyde:ferredoxin oxidoreductase were found to play important roles in CO utilization and alcohol production. Based on these findings, novel metabolic schemes are proposed for C. ljungdahlii growing on CO and/or CO2/H2. These schemes indicate that more ATP is produced during CO-fermentation than during H2-fermentation, leading to increased alcohol production.
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Affiliation(s)
- Hai-Feng Zhu
- School of Biological Engineering, Dalian Polytechnic University, Dalian, China
| | - Zi-Yong Liu
- Shandong Provincial Key Laboratory of Synthetic Biology, Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
| | - Xia Zhou
- State Key Laboratory of Shale Oil and Gas Enrichment Mechanisms and Effective Development, SINOPEC Exploration and Production Research Institute, Beijing, China
| | - Ji-Hong Yi
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Zeng-Min Lun
- State Key Laboratory of Shale Oil and Gas Enrichment Mechanisms and Effective Development, SINOPEC Exploration and Production Research Institute, Beijing, China
| | - Shu-Ning Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Wen-Zhu Tang
- School of Biological Engineering, Dalian Polytechnic University, Dalian, China
| | - Fu-Li Li
- Shandong Provincial Key Laboratory of Synthetic Biology, Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
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d'Ippolito G, Landi S, Esercizio N, Lanzilli M, Vastano M, Dipasquale L, Pradhan N, Fontana A. CO 2-Induced Transcriptional Reorganization: Molecular Basis of Capnophillic Lactic Fermentation in Thermotoga neapolitana. Front Microbiol 2020; 11:171. [PMID: 32132982 PMCID: PMC7039931 DOI: 10.3389/fmicb.2020.00171] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 01/24/2020] [Indexed: 11/25/2022] Open
Abstract
Capnophilic lactic fermentation (CLF) is a novel anaplerotic pathway able to convert sugars to lactic acid (LA) and hydrogen using CO2 as carbon enhancer in the hyperthermophilic bacterium Thermotoga neapolitana. In order to give further insights into CLF metabolic networks, we investigated the transcriptional modification induced by CO2 using a RNA-seq approach. Transcriptomic analysis revealed 1601 differentially expressed genes (DEGs) in an enriched CO2 atmosphere over a total of 1938 genes of the T. neapolitana genome. Transcription of PFOR and LDH genes belonging to the CLF pathway was up-regulated by CO2 together with 6-phosphogluconolactonase (6PGL) and 6-phosphogluconate dehydratase (EDD) of the Entner–Doudoroff (ED) pathway. The transcriptomic study also revealed up-regulation of genes coding for the flavin-based enzymes NADH-dependent reduced ferredoxin:NADP oxidoreductase (NFN) and NAD-ferredoxin oxidoreductase (RNF) that control supply of reduced ferredoxin and NADH and allow energy conservation-based sodium translocation through the cell membrane. These results support the hypothesis that CO2 induces rearrangement of the central carbon metabolism together with activation of mechanisms that increase availability of the reducing equivalents that are necessary to sustain CLF. In this view, this study reports a first rationale of the molecular basis of CLF in T. neapolitana and provides a list of target genes for the biotechnological implementation of this process.
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Affiliation(s)
- Giuliana d'Ippolito
- Bio-Organic Chemistry Unit, Institute of Biomolecular Chemistry, Italian National Research Council (CNR), Pozzuoli, Italy
| | - Simone Landi
- Bio-Organic Chemistry Unit, Institute of Biomolecular Chemistry, Italian National Research Council (CNR), Pozzuoli, Italy
| | - Nunzia Esercizio
- Bio-Organic Chemistry Unit, Institute of Biomolecular Chemistry, Italian National Research Council (CNR), Pozzuoli, Italy
| | - Mariamichella Lanzilli
- Bio-Organic Chemistry Unit, Institute of Biomolecular Chemistry, Italian National Research Council (CNR), Pozzuoli, Italy
| | - Marco Vastano
- Bio-Organic Chemistry Unit, Institute of Biomolecular Chemistry, Italian National Research Council (CNR), Pozzuoli, Italy
| | - Laura Dipasquale
- Bio-Organic Chemistry Unit, Institute of Biomolecular Chemistry, Italian National Research Council (CNR), Pozzuoli, Italy
| | - Nirakar Pradhan
- Bio-Organic Chemistry Unit, Institute of Biomolecular Chemistry, Italian National Research Council (CNR), Pozzuoli, Italy
| | - Angelo Fontana
- Bio-Organic Chemistry Unit, Institute of Biomolecular Chemistry, Italian National Research Council (CNR), Pozzuoli, Italy
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38
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Arcinas AJ, Maiocco SJ, Elliott SJ, Silakov A, Booker SJ. Ferredoxins as interchangeable redox components in support of MiaB, a radical S-adenosylmethionine methylthiotransferase. Protein Sci 2020; 28:267-282. [PMID: 30394621 DOI: 10.1002/pro.3548] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2018] [Revised: 10/29/2018] [Accepted: 10/30/2018] [Indexed: 11/10/2022]
Abstract
MiaB is a member of the methylthiotransferase subclass of the radical S-adenosylmethionine (SAM) superfamily of enzymes, catalyzing the methylthiolation of C2 of adenosines bearing an N6 -isopentenyl (i6 A) group found at position 37 in several tRNAs to afford 2-methylthio-N6 -(isopentenyl)adenosine (ms2 i6 A). MiaB uses a reduced [4Fe-4S]+ cluster to catalyze a reductive cleavage of SAM to generate a 5'-deoxyadenosyl 5'-radical (5'-dA•)-a required intermediate in its reaction-as well as an additional [4Fe-4S]2+ auxiliary cluster. In Escherichia coli and many other organisms, re-reduction of the [4Fe-4S]2+ cluster to the [4Fe-4S]+ state is accomplished by the flavodoxin reducing system. Most mechanistic studies of MiaBs have been carried out on the enzyme from Thermotoga maritima (Tm), which lacks the flavodoxin reducing system, and which is not activated by E. coli flavodoxin. However, the genome of this organism encodes five ferredoxins (TM0927, TM1175, TM1289, TM1533, and TM1815), each of which might donate the requisite electron to MiaB and perhaps to other radical SAM enzymes. The genes encoding each of these ferredoxins were cloned, and the associated proteins were isolated and shown to support turnover by Tm MiaB. In addition, TM1639, the ferredoxin-NADP+ oxidoreductase subunit α (NfnA) from Tm was overproduced and isolated and shown to provide electrons to the Tm ferredoxins during Tm MiaB turnover. The resulting reactions demonstrate improved coupling between formation of the 5'-dA• and ms2 i6 A production, indicating that only one hydrogen atom abstraction is required for the reaction.
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Affiliation(s)
- Arthur J Arcinas
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania, 16802
| | | | - Sean J Elliott
- Department of Chemistry, Boston University, Boston, Massachusetts, 02215
| | - Alexey Silakov
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania, 1680
| | - Squire J Booker
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania, 16802.,Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania, 1680.,Howard Hughes Medical Institute, The Pennsylvania State University, University Park, Pennsylvania, 16802
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Löffler M, Feldhues J, Venceslau SS, Kammler L, Grein F, Pereira IAC, Dahl C. DsrL mediates electron transfer between NADH and rDsrAB in Allochromatium vinosum. Environ Microbiol 2019; 22:783-795. [PMID: 31854015 DOI: 10.1111/1462-2920.14899] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 12/16/2019] [Accepted: 12/16/2019] [Indexed: 11/30/2022]
Abstract
Dissimilatory sulphite reductase DsrAB occurs in sulphate/sulphite-reducing prokaryotes, in sulphur disproportionators and also in sulphur oxidizers, where it functions in reverse. Predictions of physiological traits in metagenomic studies relying on the presence of dsrAB, other dsr genes or combinations thereof suffer from the lack of information on crucial Dsr proteins. The iron-sulphur flavoprotein DsrL is an example of this group. It has a documented essential function during sulphur oxidation and was recently also found in some metagenomes of probable sulphate and sulphite reducers. Here, we show that DsrL and reverse acting rDsrAB can form a complex and are copurified from the phototrophic sulphur oxidizer Allochromatium vinosum. Recombinant DsrL exhibits NAD(P)H:acceptor oxidoreductase activity with a strong preference for NADH over NADPH. In vitro, the rDsrABL complex effectively catalyses NADH-dependent sulphite reduction, which is strongly enhanced by the sulphur-binding protein DsrC. Our work reveals NAD+ as suitable in vivo electron acceptor for sulphur oxidation in organisms operating the rDsr pathway and points to reduced nicotinamide adenine dinucleotides as electron donors for sulphite reduction in sulphate/sulphite-reducing prokaryotes that contain DsrL. In addition, dsrL cannot be used as a marker distinguishing sulphate/sulphite reducers and sulphur oxidizers in metagenomic studies without further analysis.
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Affiliation(s)
- Maria Löffler
- Institut für Mikrobiologie & Biotechnologie, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | - Julia Feldhues
- Institut für Mikrobiologie & Biotechnologie, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | - Sofia S Venceslau
- Instituto de Tecnologia Química e Biológica Antonio Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Lydia Kammler
- Institut für Mikrobiologie & Biotechnologie, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | - Fabian Grein
- Institut für Mikrobiologie & Biotechnologie, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | - Inês A C Pereira
- Instituto de Tecnologia Química e Biológica Antonio Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Christiane Dahl
- Institut für Mikrobiologie & Biotechnologie, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
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40
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Low potential enzymatic hydride transfer via highly cooperative and inversely functionalized flavin cofactors. Nat Commun 2019; 10:2074. [PMID: 31061390 PMCID: PMC6502838 DOI: 10.1038/s41467-019-10078-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 04/12/2019] [Indexed: 02/01/2023] Open
Abstract
Hydride transfers play a crucial role in a multitude of biological redox reactions and are mediated by flavin, deazaflavin or nicotinamide adenine dinucleotide cofactors at standard redox potentials ranging from 0 to –340 mV. 2-Naphthoyl-CoA reductase, a key enzyme of oxygen-independent bacterial naphthalene degradation, uses a low-potential one-electron donor for the two-electron dearomatization of its substrate below the redox limit of known biological hydride transfer processes at E°’ = −493 mV. Here we demonstrate by X-ray structural analyses, QM/MM computational studies, and multiple spectroscopy/activity based titrations that highly cooperative electron transfer (n = 3) from a low-potential one-electron (FAD) to a two-electron (FMN) transferring flavin cofactor is the key to overcome the resonance stabilized aromatic system by hydride transfer in a highly hydrophobic pocket. The results evidence how the protein environment inversely functionalizes two flavins to switch from low-potential one-electron to hydride transfer at the thermodynamic limit of flavin redox chemistry. The reduction of 2-naphtoyl-CoA to 5,6 dihydro-2-naphtoyl-CoA by 2-naphtoyl-CoA reductase is below the negative redox limit usually encountered in biological hydride transfer. Here, via X-ray crystallography and spectroscopic analysis, the authors elucidated the mechanism behind this.
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41
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Miller AF, Duan HD, Varner TA, Mohamed Raseek N. Reduction midpoint potentials of bifurcating electron transfer flavoproteins. Methods Enzymol 2019; 620:365-398. [PMID: 31072494 DOI: 10.1016/bs.mie.2019.03.017] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Recently, a variety of enzymes have been found to accept electrons from NAD(P)H yet reduce lower-potential carriers such as ferredoxin and flavodoxin semiquinone, in apparent violation of thermodynamics. The reaction is favorable overall, however, because these enzymes couple the foregoing endergonic one-electron transfer to exergonic transfer of the other electron from each NAD(P)H, in a process called "flavin-based electron bifurcation." The reduction midpoint potentials (E°s) of the multiple flavins in these enzymes are critical to their mechanisms. We describe methods we have found to be useful for measuring each of the E°s of each of the flavins in bifurcating electron transfer flavoproteins.
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Affiliation(s)
- A-F Miller
- Department of Chemistry, University of Kentucky, Lexington, KY, United States.
| | - H D Duan
- Department of Chemistry, University of Kentucky, Lexington, KY, United States
| | - T A Varner
- Department of Chemistry, University of Kentucky, Lexington, KY, United States
| | - N Mohamed Raseek
- Department of Chemistry, University of Kentucky, Lexington, KY, United States
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42
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Liang J, Huang H, Wang S. Distribution, Evolution, Catalytic Mechanism, and Physiological Functions of the Flavin-Based Electron-Bifurcating NADH-Dependent Reduced Ferredoxin: NADP + Oxidoreductase. Front Microbiol 2019; 10:373. [PMID: 30881354 PMCID: PMC6405883 DOI: 10.3389/fmicb.2019.00373] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2018] [Accepted: 02/12/2019] [Indexed: 12/12/2022] Open
Abstract
NADH-dependent reduced ferredoxin:NADP+ oxidoreductase (Nfn) is an electron-bifurcating enzyme first discovered in the strict anaerobes Clostridium kluyveri and Moorella thermoacetica. In vivo, Nfn catalyzes the endergonic reduction of NADP+ with NADH coupled to the exergonic reduction of NADP+ with reduced ferredoxin. Most Nfn homologs consist of two subunits, although in certain species Nfn homologs are fused. In contrast to other electron-bifurcating enzymes, Nfn possess a simpler structure. Therefore, Nfn becomes a perfect model to determine the mechanism of flavin-based electron bifurcation, which is a novel energy coupling mode distributed among anaerobic bacteria and archaea. The crystal structures of Nfn from Thermotoga maritima and Pyrococcus furiosus are known, and studies have shown that the FAD molecule of the NfnB (b-FAD) is the site of electron bifurcation, and other cofactors, including a [2Fe2S] cluster, two [4Fe4S] clusters, and the FAD molecule on the NfnA subunit, contribute to electron transfer. Further, the short-lived anionic flavin semiquinone (ASQ) state of b-FAD is essential for electron bifurcation. Nfn homologs are widely distributed among microbes, including bacteria, archaea, and probably eukaryotes, most of which are anaerobes despite that certain species are facultative microbes and even aerobes. Moreover, potential evidence shows that lateral gene transfer may occur in the evolution of this enzyme. Nfn homologs present four different structural patterns, including the well-characterized NfnAB and three different kinds of fused Nfn homologs whose detailed properties have not been characterized. These findings indicate that gene fusion/fission and gene rearrangement may contribute to the evolution of this enzyme. Under physiological conditions, Nfn catalyzes the reduction of NADP+ with NADH and reduced ferredoxin, which is then used in certain NADPH-dependent reactions. Deletion of nfn in several microbes causes low growth and redox unbalance and may influence the distribution of fermentation products. It’s also noteworthy that different Nfn homologs perform different functions according to its circumstance. Physiological functions of Nfn indicate that it can be a potential tool in the metabolic engineering of industrial microorganisms, which can regulate the redox potential in vivo.
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Affiliation(s)
- Jiyu Liang
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
| | - Haiyan Huang
- Institute of Basic Medicine, Shandong Academy of Medical Sciences, Jinan, China
| | - Shuning Wang
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
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43
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Hydrogen-based metabolism as an ancestral trait in lineages sibling to the Cyanobacteria. Nat Commun 2019; 10:463. [PMID: 30692531 PMCID: PMC6349859 DOI: 10.1038/s41467-018-08246-y] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 12/18/2018] [Indexed: 01/06/2023] Open
Abstract
The evolution of aerobic respiration was likely linked to the origins of oxygenic Cyanobacteria. Close phylogenetic neighbors to Cyanobacteria, such as Margulisbacteria (RBX-1 and ZB3), Saganbacteria (WOR-1), Melainabacteria and Sericytochromatia, may constrain the metabolic platform in which aerobic respiration arose. Here, we analyze genomic sequences and predict that sediment-associated Margulisbacteria have a fermentation-based metabolism featuring a variety of hydrogenases, a streamlined nitrogenase, and electron bifurcating complexes involved in cycling of reducing equivalents. The genomes of ocean-associated Margulisbacteria encode an electron transport chain that may support aerobic growth. Some Saganbacteria genomes encode various hydrogenases, and others may be able to use O2 under certain conditions via a putative novel type of heme copper O2 reductase. Similarly, Melainabacteria have diverse energy metabolisms and are capable of fermentation and aerobic or anaerobic respiration. The ancestor of all these groups may have been an anaerobe in which fermentation and H2 metabolism were central metabolic features. The ability to use O2 as a terminal electron acceptor must have been subsequently acquired by these lineages. Most cyanobacteria are oxygenic photoautotrophs, and fermenters under dark anoxic conditions. Here, the authors analyse genomic sequences of related uncultivated bacteria, inferring their metabolic potential, and supporting that their common ancestor was an anaerobe capable of fermentation and H2 metabolism.
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44
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Yuly JL, Lubner CE, Zhang P, Beratan DN, Peters JW. Electron bifurcation: progress and grand challenges. Chem Commun (Camb) 2019; 55:11823-11832. [DOI: 10.1039/c9cc05611d] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Electron bifurcation moves electrons from a two-electron donor to reduce two spatially separated one-electron acceptors.
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Affiliation(s)
| | | | - Peng Zhang
- Department of Chemistry
- Duke University
- Durham
- USA
| | - David N. Beratan
- Department of Physics
- Duke University
- Durham
- USA
- Department of Chemistry
| | - John W. Peters
- Institute of Biological Chemistry
- Washington State University
- Pullman
- USA
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45
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Schuchmann K, Chowdhury NP, Müller V. Complex Multimeric [FeFe] Hydrogenases: Biochemistry, Physiology and New Opportunities for the Hydrogen Economy. Front Microbiol 2018; 9:2911. [PMID: 30564206 PMCID: PMC6288185 DOI: 10.3389/fmicb.2018.02911] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Accepted: 11/13/2018] [Indexed: 12/03/2022] Open
Abstract
Hydrogenases are key enzymes of the energy metabolism of many microorganisms. Especially in anoxic habitats where molecular hydrogen (H2) is an important intermediate, these enzymes are used to expel excess reducing power by reducing protons or they are used for the oxidation of H2 as energy and electron source. Despite the fact that hydrogenases catalyze the simplest chemical reaction of reducing two protons with two electrons it turned out that they are often parts of multimeric enzyme complexes catalyzing complex chemical reactions with a multitude of functions in the metabolism. Recent findings revealed multimeric hydrogenases with so far unknown functions particularly in bacteria from the class Clostridia. The discovery of [FeFe] hydrogenases coupled to electron bifurcating subunits solved the enigma of how the otherwise highly endergonic reduction of the electron carrier ferredoxin can be carried out and how H2 production from NADH is possible. Complexes of [FeFe] hydrogenases with formate dehydrogenases revealed a novel enzymatic coupling of the two electron carriers H2 and formate. These novel hydrogenase enzyme complex could also contribute to biotechnological H2 production and H2 storage, both processes essential for an envisaged economy based on H2 as energy carrier.
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Affiliation(s)
- Kai Schuchmann
- Molecular Microbiology and Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Frankfurt am Main, Germany
| | - Nilanjan Pal Chowdhury
- Molecular Microbiology and Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Frankfurt am Main, Germany
| | - Volker Müller
- Molecular Microbiology and Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Frankfurt am Main, Germany
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46
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Poudel S, Dunham EC, Lindsay MR, Amenabar MJ, Fones EM, Colman DR, Boyd ES. Origin and Evolution of Flavin-Based Electron Bifurcating Enzymes. Front Microbiol 2018; 9:1762. [PMID: 30123204 PMCID: PMC6085437 DOI: 10.3389/fmicb.2018.01762] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2018] [Accepted: 07/13/2018] [Indexed: 12/31/2022] Open
Abstract
Twelve evolutionarily unrelated oxidoreductases form enzyme complexes that catalyze the simultaneous coupling of exergonic and endergonic oxidation–reduction reactions to circumvent thermodynamic barriers and minimize free energy loss in a process known as flavin-based electron bifurcation. Common to these 12 bifurcating (Bf) enzymes are protein-bound flavin, the proposed site of bifurcation, and the electron carrier ferredoxin. Despite the documented role of Bf enzymes in balancing the redox state of intracellular electron carriers and in improving the efficiency of cellular metabolism, a comprehensive description of the diversity and evolutionary history of Bf enzymes is lacking. Here, we report the taxonomic distribution, functional diversity, and evolutionary history of Bf enzyme homologs in 4,588 archaeal, bacterial, and eukaryal genomes and 3,136 community metagenomes. Bf homologs were primarily detected in the genomes of anaerobes, including those of sulfate-reducers, acetogens, fermenters, and methanogens. Phylogenetic analyses of Bf enzyme catalytic subunits (oxidoreductases) suggest they were not a property of the Last Universal Common Ancestor of Archaea and Bacteria, which is consistent with the limited and unique taxonomic distributions of enzyme homologs among genomes. Further, phylogenetic analyses of oxidoreductase subunits reveal that non-Bf homologs predate Bf homologs. These observations indicate that multiple independent recruitments of flavoproteins to existing oxidoreductases enabled coupling of numerous new electron Bf reactions. Consistent with the role of these enzymes in the energy metabolism of anaerobes, homologs of Bf enzymes were enriched in metagenomes from subsurface environments relative to those from surface environments. Phylogenetic analyses of homologs from metagenomes reveal that the earliest evolving homologs of most Bf enzymes are from subsurface environments, including fluids from subsurface rock fractures and hydrothermal systems. Collectively, these data suggest strong selective pressures drove the emergence of Bf enzyme complexes via recruitment of flavoproteins that allowed for an increase in the efficiency of cellular metabolism and improvement in energy capture in anaerobes inhabiting a variety of subsurface anoxic habitats where the energy yield of oxidation-reduction reactions is generally low.
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Affiliation(s)
- Saroj Poudel
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT, United States
| | - Eric C Dunham
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT, United States
| | - Melody R Lindsay
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT, United States
| | - Maximiliano J Amenabar
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT, United States
| | - Elizabeth M Fones
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT, United States
| | - Daniel R Colman
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT, United States
| | - Eric S Boyd
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT, United States
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47
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Peters JW, Beratan DN, Bothner B, Dyer RB, Harwood CS, Heiden ZM, Hille R, Jones AK, King PW, Lu Y, Lubner CE, Minteer SD, Mulder DW, Raugei S, Schut GJ, Seefeldt LC, Tokmina-Lukaszewska M, Zadvornyy OA, Zhang P, Adams MW. A new era for electron bifurcation. Curr Opin Chem Biol 2018; 47:32-38. [PMID: 30077080 DOI: 10.1016/j.cbpa.2018.07.026] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Revised: 06/16/2018] [Accepted: 07/18/2018] [Indexed: 11/17/2022]
Abstract
Electron bifurcation, or the coupling of exergonic and endergonic oxidation-reduction reactions, was discovered by Peter Mitchell and provides an elegant mechanism to rationalize and understand the logic that underpins the Q cycle of the respiratory chain. Thought to be a unique reaction of respiratory complex III for nearly 40 years, about a decade ago Wolfgang Buckel and Rudolf Thauer discovered that flavin-based electron bifurcation is also an important component of anaerobic microbial metabolism. Their discovery spawned a surge of research activity, providing a basis to understand flavin-based bifurcation, forging fundamental parallels with Mitchell's Q cycle and leading to the proposal of metal-based bifurcating enzymes. New insights into the mechanism of electron bifurcation provide a foundation to establish the unifying principles and essential elements of this fascinating biochemical phenomenon.
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Affiliation(s)
- John W Peters
- Institute of Biological Chemistry, Washington State University, Pullman WA 99163, United States; Pacific Northwest National Laboratory, Richland, WA 99352, United States.
| | - David N Beratan
- Department of Chemistry and Department of Physics, Duke University, Durham, NC 27708, United States; Department of Biochemistry, Duke University, Durham, NC 27710, United States
| | - Brian Bothner
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, United States
| | - R Brian Dyer
- Department of Chemistry, Emory University, Atlanta, GA 30322, United States
| | - Caroline S Harwood
- Department of Microbiology, University of Washington, Seattle, WA 98195, United States
| | - Zachariah M Heiden
- Department of Chemistry, Washington State University, Pullman WA 99163, United States
| | - Russ Hille
- Biochemistry Department, University of California at Riverside, Riverside, CA 92521, United States
| | - Anne K Jones
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, United States
| | - Paul W King
- National Renewable Energy Laboratory, Golden, CO 8040, United States
| | - Yi Lu
- Pacific Northwest National Laboratory, Richland, WA 99352, United States; Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
| | - Carolyn E Lubner
- National Renewable Energy Laboratory, Golden, CO 8040, United States
| | - Shelley D Minteer
- Department of Chemistry, University of Utah, Salt Lake City, UT 84112, United States
| | - David W Mulder
- National Renewable Energy Laboratory, Golden, CO 8040, United States
| | - Simone Raugei
- Institute of Biological Chemistry, Washington State University, Pullman WA 99163, United States; Pacific Northwest National Laboratory, Richland, WA 99352, United States
| | - Gerrit J Schut
- Department of Biochemistry & Molecular Biology, University of Georgia, Athens, GA 30602, United States
| | - Lance C Seefeldt
- Pacific Northwest National Laboratory, Richland, WA 99352, United States; Department of Chemistry and Biochemistry, Utah State University, Logan, UT 84322, United States
| | | | - Oleg A Zadvornyy
- Institute of Biological Chemistry, Washington State University, Pullman WA 99163, United States
| | - Peng Zhang
- Department of Biochemistry, Duke University, Durham, NC 27710, United States
| | - Michael Ww Adams
- Department of Biochemistry & Molecular Biology, University of Georgia, Athens, GA 30602, United States
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48
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Müller V, Chowdhury NP, Basen M. Electron Bifurcation: A Long-Hidden Energy-Coupling Mechanism. Annu Rev Microbiol 2018; 72:331-353. [PMID: 29924687 DOI: 10.1146/annurev-micro-090816-093440] [Citation(s) in RCA: 81] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
A decade ago, a novel mechanism to drive thermodynamically unfavorable redox reactions was discovered that is used in prokaryotes to drive endergonic electron transfer reactions by a direct coupling to an exergonic redox reaction in one soluble enzyme complex. This process is referred to as flavin-based electron bifurcation, or FBEB. An important function of FBEB is that it allows the generation of reduced low-potential ferredoxin (Fdred) from comparably high-potential electron donors such as NADH or molecular hydrogen (H2). Fdred is then the electron donor for anaerobic respiratory chains leading to the synthesis of ATP. In many metabolic scenarios, Fd is reduced by metabolic oxidoreductases and Fdred then drives endergonic metabolic reactions such as H2 production by the reverse, electron confurcation. FBEB is energetically more economical than ATP hydrolysis or reverse electron transport as a driving force for endergonic redox reactions; thus, it does "save" cellular ATP. It is essential for autotrophic growth at the origin of life and also allows for heterotrophic growth on certain low-energy substrates.
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Affiliation(s)
- Volker Müller
- Department of Molecular Microbiology and Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University Frankfurt/Main, 60438 Frankfurt, Germany;
| | - Nilanjan Pal Chowdhury
- Department of Molecular Microbiology and Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University Frankfurt/Main, 60438 Frankfurt, Germany;
| | - Mirko Basen
- Department of Molecular Microbiology and Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University Frankfurt/Main, 60438 Frankfurt, Germany;
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Buckel W, Thauer RK. Flavin-Based Electron Bifurcation, A New Mechanism of Biological Energy Coupling. Chem Rev 2018; 118:3862-3886. [PMID: 29561602 DOI: 10.1021/acs.chemrev.7b00707] [Citation(s) in RCA: 189] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
There are two types of electron bifurcation (EB), either quinone- or flavin-based (QBEB/FBEB), that involve reduction of a quinone or flavin by a two-electron transfer and two reoxidations by a high- and low-potential one-electron acceptor with a reactive semiquinone intermediate. In QBEB, the reduced low-potential acceptor (cytochrome b) is exclusively used to generate ΔμH+. In FBEB, the "energy-rich" low-potential reduced ferredoxin or flavodoxin has dual function. It can give rise to ΔμH+/Na+ via a ferredoxin:NAD reductase (Rnf) or ferredoxin:proton reductase (Ech) or conducts difficult reductions such as CO2 to CO. The QBEB membrane complexes are similar in structure and function and occur in all domains of life. In contrast, FBEB complexes are soluble and occur only in strictly anaerobic bacteria and archaea (FixABCX being an exception). The FBEB complexes constitute a group consisting of four unrelated families that contain (1) electron-transferring flavoproteins (EtfAB), (2) NAD(P)H dehydrogenase (NuoF homologues), (3) heterodisulfide reductase (HdrABC) or HdrABC homologues, and (4) NADH-dependent ferredoxin:NADP reductase (NfnAB). The crystal structures and electron transport of EtfAB-butyryl-CoA dehydrogenase and NfnAB are compared with those of complex III of the respiratory chain (cytochrome bc1), whereby unexpected common features have become apparent.
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Affiliation(s)
- Wolfgang Buckel
- Fachbereich Biologie , Philipps-Universität , 35032 Marburg , Germany.,Max-Planck-Institut für Terrestrische Mikrobiologie , 35043 Marburg , Germany
| | - Rudolf K Thauer
- Fachbereich Biologie , Philipps-Universität , 35032 Marburg , Germany.,Max-Planck-Institut für Terrestrische Mikrobiologie , 35043 Marburg , Germany
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Buckel W, Thauer RK. Flavin-Based Electron Bifurcation, Ferredoxin, Flavodoxin, and Anaerobic Respiration With Protons (Ech) or NAD + (Rnf) as Electron Acceptors: A Historical Review. Front Microbiol 2018; 9:401. [PMID: 29593673 PMCID: PMC5861303 DOI: 10.3389/fmicb.2018.00401] [Citation(s) in RCA: 199] [Impact Index Per Article: 33.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2017] [Accepted: 02/21/2018] [Indexed: 12/19/2022] Open
Abstract
Flavin-based electron bifurcation is a newly discovered mechanism, by which a hydride electron pair from NAD(P)H, coenzyme F420H2, H2, or formate is split by flavoproteins into one-electron with a more negative reduction potential and one with a more positive reduction potential than that of the electron pair. Via this mechanism microorganisms generate low- potential electrons for the reduction of ferredoxins (Fd) and flavodoxins (Fld). The first example was described in 2008 when it was found that the butyryl-CoA dehydrogenase-electron-transferring flavoprotein complex (Bcd-EtfAB) of Clostridium kluyveri couples the endergonic reduction of ferredoxin (E0′ = −420 mV) with NADH (−320 mV) to the exergonic reduction of crotonyl-CoA to butyryl-CoA (−10 mV) with NADH. The discovery was followed by the finding of an electron-bifurcating Fd- and NAD-dependent [FeFe]-hydrogenase (HydABC) in Thermotoga maritima (2009), Fd-dependent transhydrogenase (NfnAB) in various bacteria and archaea (2010), Fd- and H2-dependent heterodisulfide reductase (MvhADG-HdrABC) in methanogenic archaea (2011), Fd- and NADH-dependent caffeyl-CoA reductase (CarCDE) in Acetobacterium woodii (2013), Fd- and NAD-dependent formate dehydrogenase (HylABC-FdhF2) in Clostridium acidi-urici (2013), Fd- and NADP-dependent [FeFe]-hydrogenase (HytA-E) in Clostridium autoethanogrenum (2013), Fd(?)- and NADH-dependent methylene-tetrahydrofolate reductase (MetFV-HdrABC-MvhD) in Moorella thermoacetica (2014), Fd- and NAD-dependent lactate dehydrogenase (LctBCD) in A. woodii (2015), Fd- and F420H2-dependent heterodisulfide reductase (HdrA2B2C2) in Methanosarcina acetivorans (2017), and Fd- and NADH-dependent ubiquinol reductase (FixABCX) in Azotobacter vinelandii (2017). The electron-bifurcating flavoprotein complexes known to date fall into four groups that have evolved independently, namely those containing EtfAB (CarED, LctCB, FixBA) with bound FAD, a NuoF homolog (HydB, HytB, or HylB) harboring FMN, NfnB with bound FAD, or HdrA harboring FAD. All these flavoproteins are cytoplasmic except for the membrane-associated protein FixABCX. The organisms—in which they have been found—are strictly anaerobic microorganisms except for the aerobe A. vinelandii. The electron-bifurcating complexes are involved in a variety of processes such as butyric acid fermentation, methanogenesis, acetogenesis, anaerobic lactate oxidation, dissimilatory sulfate reduction, anaerobic- dearomatization, nitrogen fixation, and CO2 fixation. They contribute to energy conservation via the energy-converting ferredoxin: NAD+ reductase complex Rnf or the energy-converting ferredoxin-dependent hydrogenase complex Ech. This Review describes how this mechanism was discovered.
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Affiliation(s)
- Wolfgang Buckel
- Laboratory for Microbiology, Faculty of Biology, Philipps-Universität Marburg, Marburg, Germany
| | - Rudolf K Thauer
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
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