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Li MY, Wang YQ, Ying YL, Long YT. Revealing the transient conformations of a single flavin adenine dinucleotide using an aerolysin nanopore. Chem Sci 2019; 10:10400-10404. [PMID: 32110330 PMCID: PMC6988595 DOI: 10.1039/c9sc03163d] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Accepted: 09/20/2019] [Indexed: 12/13/2022] Open
Abstract
Flavin adenine dinucleotide (FAD) as a cofactor is involved in numerous important metabolic pathways where the biological function is intrinsically related to its transient conformations. The confined space of enzymes requires FAD set in its specific intermediate conformation. However, conventional methods only detect stable conformations of FAD molecules, while transient intermediates are hidden in ensemble measurements. There still exists a challenge to uncover the transient conformation of each FAD molecule, which hinders the understanding of the structure-activity relationship of the FAD mechanism. Here, we employ the electrochemically confined space of an aerolysin nanopore to directly characterize a series of transient conformations of every individual FAD. Based on distinguishable current blockages, the "stack", "open", and four quasi-stacked FADs are clearly determined in solution, which is further confirmed by temperature-dependent experiments and mutant aerolysin assay. Combined with molecular dynamics simulations, we achieved a direct correlation between the residual current ratio (I/I 0) and FAD backbone angle. These results would facilitate further understanding of the structure-activity relationship in the flavoprotein.
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Affiliation(s)
- Meng-Yin Li
- State Key Laboratory of Analytical Chemistry for Life Science , School of Chemistry and Chemical Engineering , 210023 , Nanjing , P. R. China . .,School of Chemistry and Molecule Engineering , East China University of Science and Technology , 200237 , Shanghai , P. R. China
| | - Ya-Qian Wang
- School of Chemistry and Molecule Engineering , East China University of Science and Technology , 200237 , Shanghai , P. R. China
| | - Yi-Lun Ying
- State Key Laboratory of Analytical Chemistry for Life Science , School of Chemistry and Chemical Engineering , 210023 , Nanjing , P. R. China .
| | - Yi-Tao Long
- State Key Laboratory of Analytical Chemistry for Life Science , School of Chemistry and Chemical Engineering , 210023 , Nanjing , P. R. China .
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Mohamed-Raseek N, Duan HD, Hildebrandt P, Mroginski MA, Miller AF. Spectroscopic, thermodynamic and computational evidence of the locations of the FADs in the nitrogen fixation-associated electron transfer flavoprotein. Chem Sci 2019; 10:7762-7772. [PMID: 31588324 PMCID: PMC6764259 DOI: 10.1039/c9sc00942f] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2019] [Accepted: 06/24/2019] [Indexed: 01/15/2023] Open
Abstract
Flavin-based electron bifurcation allows enzymes to redistribute energy among electrons by coupling endergonic and exergonic electron transfer reactions. Diverse bifurcating enzymes employ a two-flavin electron transfer flavoprotein (ETF) that accepts hydride from NADH at a flavin (the so-called bifurcating FAD, Bf-FAD). The Bf-FAD passes one electron exergonically to a second flavin thereby assuming a reactive semiquinone state able to reduce ferredoxin or flavodoxin semiquinone. The flavin that accepts one electron and passes it on via exergonic electron transfer is known as the electron transfer FAD (ET-FAD) and is believed to correspond to the single FAD present in canonical ETFs, in domain II. The Bf-FAD is believed to be the one that is unique to bifurcating ETFs, bound between domains I and III. This very reasonable model has yet to be challenged experimentally. Herein we used site-directed mutagenesis to disrupt FAD binding to the presumed Bf site between domains I and III, in the Bf-ETF from Rhodopseudomonas palustris (RpaETF). The resulting protein contained only 0.80 ± 0.05 FAD, plus 1.21 ± 0.04 bound AMP as in canonical ETFs. The flavin was not subject to reduction by NADH, confirming absence of Bf-FAD. The retained FAD displayed visible circular dichroism (CD) similar to that of the ET-FAD of RpaETF. Likewise, the mutant underwent two sequential one-electron reductions forming and then consuming anionic semiquinone, reproducing the reactivity of the ET-FAD. These data confirm that the retained FAD in domain II corresponds the ET-FAD. Quantum chemical calculations of the absorbance and CD spectra of each of WT RpaETF's two flavins reproduced the observed differences between their CD and absorbance signatures. The calculations for the flavin bound in domain II agreed better with the spectra of the ET-flavin, and those calculated based on the flavin between domains I and III agreed better with spectra of the Bf-flavin. Thus calculations independently confirm the locations of each flavin. We conclude that the site in domain II harbours the ET-FAD whereas the mutated site between domains I and III is the Bf-FAD site, confirming the accepted model by two different tests.
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Affiliation(s)
- Nishya Mohamed-Raseek
- Dept. Chemistry , University of Kentucky , 505 Rose Street , Lexington , KY 40506-0055 , USA .
| | - H Diessel Duan
- Dept. Chemistry , University of Kentucky , 505 Rose Street , Lexington , KY 40506-0055 , USA .
| | - Peter Hildebrandt
- Max Volmer Laboratorum für Biophysikalische Chemie , Technische Universität - Berlin , Sekr. PC 14, 135 Straße des 17. Juni , 10623 Berlin , Germany
| | - Maria Andrea Mroginski
- Max Volmer Laboratorum für Biophysikalische Chemie , Technische Universität - Berlin , Sekr. PC 14, 135 Straße des 17. Juni , 10623 Berlin , Germany
| | - Anne-Frances Miller
- Dept. Chemistry , University of Kentucky , 505 Rose Street , Lexington , KY 40506-0055 , USA .
- Max Volmer Laboratorum für Biophysikalische Chemie , Technische Universität - Berlin , Sekr. PC 14, 135 Straße des 17. Juni , 10623 Berlin , Germany
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53
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Swuec P, Chaves-Sanjuan A, Camilloni C, Vanoni MA, Bolognesi M. Cryo-EM Structures of Azospirillum brasilense Glutamate Synthase in Its Oligomeric Assemblies. J Mol Biol 2019; 431:4523-4526. [PMID: 31473159 DOI: 10.1016/j.jmb.2019.08.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 08/13/2019] [Accepted: 08/19/2019] [Indexed: 10/26/2022]
Abstract
Bacterial NADPH-dependent glutamate synthase (GltS) is a complex iron-sulfur flavoprotein that catalyzes the reductive synthesis of two L-Glu molecules from L-Gln and 2-oxo-glutarate. GltS functional unit hosts an α-subunit (αGltS) and a β-subunit (βGltS) that assemble in different αβ oligomers in solution. Here, we present the cryo-electron microscopy structures of Azospirillum brasilense GltS in four different oligomeric states (α4β3, α4β4, α6β4 and α6β6, in the 3.5- to 4.1-Å resolution range). Our study provides a comprehensive GltS model that details the inter-protomeric assemblies and allows unequivocal location of the FAD cofactor and of two electron transfer [4Fe-4S]+1,+2 clusters within βGltS.
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Affiliation(s)
- Paolo Swuec
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133 Milano, Italy; Centro di Ricerca Pediatrica Romeo ed Enrica Invernizzi, Università degli Studi di Milano, Via Celoria 26, 20133 Milano, Italy
| | - Antonio Chaves-Sanjuan
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133 Milano, Italy
| | - Carlo Camilloni
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133 Milano, Italy
| | - Maria Antonietta Vanoni
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133 Milano, Italy
| | - Martino Bolognesi
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133 Milano, Italy; Centro di Ricerca Pediatrica Romeo ed Enrica Invernizzi, Università degli Studi di Milano, Via Celoria 26, 20133 Milano, Italy.
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54
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Identification of a Formate-Dependent Uric Acid Degradation Pathway in Escherichia coli. J Bacteriol 2019; 201:JB.00573-18. [PMID: 30885932 DOI: 10.1128/jb.00573-18] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Accepted: 02/28/2019] [Indexed: 01/31/2023] Open
Abstract
Purine is a nitrogen-containing compound that is abundant in nature. In organisms that utilize purine as a nitrogen source, purine is converted to uric acid, which is then converted to allantoin. Allantoin is then converted to ammonia. In Escherichia coli, neither urate-degrading activity nor a gene encoding an enzyme homologous to the known urate-degrading enzymes had previously been found. Here, we demonstrate urate-degrading activity in E. coli We first identified aegA as an E. coli gene involved in oxidative stress tolerance. An examination of gene expression revealed that both aegA and its paralog ygfT are expressed under both microaerobic and anaerobic conditions. The ygfT gene is localized within a chromosomal gene cluster presumably involved in purine catabolism. Accordingly, the expression of ygfT increased in the presence of exogenous uric acid, suggesting that ygfT is involved in urate degradation. Examination of the change of uric acid levels in the growth medium with time revealed urate-degrading activity under microaerobic and anaerobic conditions in the wild-type strain but not in the aegA ygfT double-deletion mutant. Furthermore, AegA- and YgfT-dependent urate-degrading activity was detected only in the presence of formate and formate dehydrogenase H. Collectively, these observations indicate the presence of urate-degrading activity in E. coli that is operational under microaerobic and anaerobic conditions. The activity requires formate, formate dehydrogenase H, and either aegA or ygfT We also identified other putative genes which are involved not only in formate-dependent but also in formate-independent urate degradation and may function in the regulation or cofactor synthesis in purine catabolism.IMPORTANCE The metabolic pathway of uric acid degradation to date has been elucidated only in aerobic environments and is not understood in anaerobic and microaerobic environments. In the current study, we showed that Escherichia coli, a facultative anaerobic organism, uses uric acid as a sole source of nitrogen under anaerobic and microaerobic conditions. We also showed that formate, formate dehydrogenase H, and either AegA or YgfT are involved in uric acid degradation. We propose that formate may act as an electron donor for a uric acid-degrading enzyme in this bacterium.
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55
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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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56
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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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57
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Distinct Physiological Roles of the Three Ferredoxins Encoded in the Hyperthermophilic Archaeon Thermococcus kodakarensis. mBio 2019; 10:mBio.02807-18. [PMID: 30837343 PMCID: PMC6401487 DOI: 10.1128/mbio.02807-18] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
High-energy electrons liberated during catabolic processes can be exploited for energy-conserving mechanisms. Maximal energy gains demand these valuable electrons be accurately shuttled from electron donor to appropriate electron acceptor. Proteinaceous electron carriers such as ferredoxins offer opportunities to exploit specific ferredoxin partnerships to ensure that electron flux to critical physiological pathways is aligned with maximal energy gains. Most species encode many ferredoxin isoforms, but very little is known about the role of individual ferredoxins in most systems. Our results detail that ferredoxin isoforms make largely unique and distinct protein interactions in vivo and that flux through one ferredoxin often cannot be recovered by flux through a different ferredoxin isoform. The results obtained more broadly suggest that ferredoxin isoforms throughout biological life have evolved not as generic electron shuttles, but rather serve as selective couriers of valuable low-potential electrons from select electron donors to desirable electron acceptors. Control of electron flux is critical in both natural and bioengineered systems to maximize energy gains. Both small molecules and proteins shuttle high-energy, low-potential electrons liberated during catabolism through diverse metabolic landscapes. Ferredoxin (Fd) proteins—an abundant class of Fe-S-containing small proteins—are essential in many species for energy conservation and ATP production strategies. It remains difficult to model electron flow through complicated metabolisms and in systems in which multiple Fd proteins are present. The overlap of activity and/or limitations of electron flux through each Fd can limit physiology and metabolic engineering strategies. Here we establish the interplay, reactivity, and physiological role(s) of the three ferredoxin proteins in the model hyperthermophile Thermococcus kodakarensis. We demonstrate that the three loci encoding known Fds are subject to distinct regulatory mechanisms and that specific Fds are utilized to shuttle electrons to separate respiratory and energy production complexes during different physiological states. The results obtained argue that unique physiological roles have been established for each Fd and that continued use of T. kodakarensis and related hydrogen-evolving species as bioengineering platforms must account for the distinct Fd partnerships that limit flux to desired electron acceptors. Extrapolating our results more broadly, the retention of multiple Fd isoforms in most species argues that specialized Fd partnerships are likely to influence electron flux throughout biology.
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58
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Schut GJ, Mohamed-Raseek N, Tokmina-Lukaszewska M, Mulder DW, Nguyen DMN, Lipscomb GL, Hoben JP, Patterson A, Lubner CE, King PW, Peters JW, Bothner B, Miller AF, Adams MWW. The catalytic mechanism of electron-bifurcating electron transfer flavoproteins (ETFs) involves an intermediary complex with NAD<sup/>. J Biol Chem 2019; 294:3271-3283. [PMID: 30567738 PMCID: PMC6398123 DOI: 10.1074/jbc.ra118.005653] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 12/11/2018] [Indexed: 12/20/2022] Open
Abstract
Electron bifurcation plays a key role in anaerobic energy metabolism, but it is a relatively new discovery, and only limited mechanistic information is available on the diverse enzymes that employ it. Herein, we focused on the bifurcating electron transfer flavoprotein (ETF) from the hyperthermophilic archaeon Pyrobaculum aerophilum The EtfABCX enzyme complex couples NADH oxidation to the endergonic reduction of ferredoxin and exergonic reduction of menaquinone. We developed a model for the enzyme structure by using nondenaturing MS, cross-linking, and homology modeling in which EtfA, -B, and -C each contained FAD, whereas EtfX contained two [4Fe-4S] clusters. On the basis of analyses using transient absorption, EPR, and optical titrations with NADH or inorganic reductants with and without NAD+, we propose a catalytic cycle involving formation of an intermediary NAD+-bound complex. A charge transfer signal revealed an intriguing interplay of flavin semiquinones and a protein conformational change that gated electron transfer between the low- and high-potential pathways. We found that despite a common bifurcating flavin site, the proposed EtfABCX catalytic cycle is distinct from that of the genetically unrelated bifurcating NADH-dependent ferredoxin NADP+ oxidoreductase (NfnI). The two enzymes particularly differed in the role of NAD+, the resting and bifurcating-ready states of the enzymes, how electron flow is gated, and the two two-electron cycles constituting the overall four-electron reaction. We conclude that P. aerophilum EtfABCX provides a model catalytic mechanism that builds on and extends previous studies of related bifurcating ETFs and can be applied to the large bifurcating ETF family.
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Affiliation(s)
- Gerrit J Schut
- From the Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602-7229
| | | | | | - David W Mulder
- the Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401, and
| | - Diep M N Nguyen
- From the Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602-7229
| | - Gina L Lipscomb
- From the Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602-7229
| | - John P Hoben
- the Department of Chemistry, University of Kentucky, Lexington, Kentucky 40506
| | - Angela Patterson
- the Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717
| | - Carolyn E Lubner
- the Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401, and
| | - Paul W King
- the Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401, and
| | - John W Peters
- the Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164
| | - Brian Bothner
- the Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717
| | - Anne-Frances Miller
- the Department of Chemistry, University of Kentucky, Lexington, Kentucky 40506
| | - Michael W W Adams
- From the Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602-7229,
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59
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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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60
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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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61
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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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63
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Patterson A, Tokmina-Lukaszewska M, Bothner B. Probing Cascade complex composition and stability using native mass spectrometry techniques. Methods Enzymol 2018; 616:87-116. [PMID: 30691656 DOI: 10.1016/bs.mie.2018.10.018] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Adaptive prokaryotic immune systems rely on clustered regularly interspaced short palindromic repeats and their associated genes to provide the components necessary to clear infection by foreign genetic elements. These immune systems are based on highly specific nucleases that bind DNA or RNA and, upon sequence recognition, degrade the bound nucleic acid. Because of their specificity, CRISPR-Cas systems are being co-opted to edit genes in eukaryotic cells. While the general function of these systems is well understood, an understanding of mechanistic details to facilitate engineering and application to this new arena remains a topic of intense study. Here, we present two methods that have been successfully used to study the structure and mechanism of the Type IE CRISPR system, Cascade, from Escherichia coli. We provide the protocol for a typical native mass spectrometry experiment which, because it allows for analysis of a protein complex without disruption of the noncovalent interactions within the complex, can be used to determine complex composition, architecture, and relative affinity between subunits. We, also, provide the protocol for intact protein hydrogen-deuterium exchange mass spectrometry, which provides insight into the overall conformational stability of the complex and changes in complex stability based on conditions such as substrate binding. Investigating the solution-phase structure, stability, and dynamics of these complexes improves the overall understanding of the mechanism facilitating engineered adjustments to function or utility.
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Affiliation(s)
- Angela Patterson
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, United States
| | | | - Brian Bothner
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, United States.
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64
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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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Yung YL, Chen P, Nealson K, Atreya S, Beckett P, Blank JG, Ehlmann B, Eiler J, Etiope G, Ferry JG, Forget F, Gao P, Hu R, Kleinböhl A, Klusman R, Lefèvre F, Miller C, Mischna M, Mumma M, Newman S, Oehler D, Okumura M, Oremland R, Orphan V, Popa R, Russell M, Shen L, Sherwood Lollar B, Staehle R, Stamenković V, Stolper D, Templeton A, Vandaele AC, Viscardy S, Webster CR, Wennberg PO, Wong ML, Worden J. Methane on Mars and Habitability: Challenges and Responses. ASTROBIOLOGY 2018; 18:1221-1242. [PMID: 30234380 PMCID: PMC6205098 DOI: 10.1089/ast.2018.1917] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Accepted: 06/12/2018] [Indexed: 05/05/2023]
Abstract
Recent measurements of methane (CH4) by the Mars Science Laboratory (MSL) now confront us with robust data that demand interpretation. Thus far, the MSL data have revealed a baseline level of CH4 (∼0.4 parts per billion by volume [ppbv]), with seasonal variations, as well as greatly enhanced spikes of CH4 with peak abundances of ∼7 ppbv. What do these CH4 revelations with drastically different abundances and temporal signatures represent in terms of interior geochemical processes, or is martian CH4 a biosignature? Discerning how CH4 generation occurs on Mars may shed light on the potential habitability of Mars. There is no evidence of life on the surface of Mars today, but microbes might reside beneath the surface. In this case, the carbon flux represented by CH4 would serve as a link between a putative subterranean biosphere on Mars and what we can measure above the surface. Alternatively, CH4 records modern geochemical activity. Here we ask the fundamental question: how active is Mars, geochemically and/or biologically? In this article, we examine geological, geochemical, and biogeochemical processes related to our overarching question. The martian atmosphere and surface are an overwhelmingly oxidizing environment, and life requires pairing of electron donors and electron acceptors, that is, redox gradients, as an essential source of energy. Therefore, a fundamental and critical question regarding the possibility of life on Mars is, "Where can we find redox gradients as energy sources for life on Mars?" Hence, regardless of the pathway that generates CH4 on Mars, the presence of CH4, a reduced species in an oxidant-rich environment, suggests the possibility of redox gradients supporting life and habitability on Mars. Recent missions such as ExoMars Trace Gas Orbiter may provide mapping of the global distribution of CH4. To discriminate between abiotic and biotic sources of CH4 on Mars, future studies should use a series of diagnostic geochemical analyses, preferably performed below the ground or at the ground/atmosphere interface, including measurements of CH4 isotopes, methane/ethane ratios, H2 gas concentration, and species such as acetic acid. Advances in the fields of Mars exploration and instrumentation will be driven, augmented, and supported by an improved understanding of atmospheric chemistry and dynamics, deep subsurface biogeochemistry, astrobiology, planetary geology, and geophysics. Future Mars exploration programs will have to expand the integration of complementary areas of expertise to generate synergistic and innovative ideas to realize breakthroughs in advancing our understanding of the potential of life and habitable conditions having existed on Mars. In this spirit, we conducted a set of interdisciplinary workshops. From this series has emerged a vision of technological, theoretical, and methodological innovations to explore the martian subsurface and to enhance spatial tracking of key volatiles, such as CH4.
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Affiliation(s)
- Yuk L. Yung
- California Institute of Technology, Pasadena, California
- NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California
| | - Pin Chen
- NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California
| | | | | | | | - Jennifer G. Blank
- NASA Ames Research Center, Blue Marble Space Institute of Science, Mountain View, California
| | - Bethany Ehlmann
- California Institute of Technology, Pasadena, California
- NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California
| | - John Eiler
- California Institute of Technology, Pasadena, California
| | - Giuseppe Etiope
- Istituto Nazionale di Geofisica e Vulcanologia, Rome, Italy
- Faculty of Environmental Science and Engineering, Babes-Bolyai University, Cluj-Napoca, Romania
| | - James G. Ferry
- The Pennsylvania State University, University Park, Pennsylvania
| | - Francois Forget
- Laboratoire de Météorologie Dynamique, Institut Pierre Simon Laplace, CNRS, Paris, France
| | - Peter Gao
- University of California, Berkeley, California
| | - Renyu Hu
- NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California
| | - Armin Kleinböhl
- NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California
| | | | - Franck Lefèvre
- Laboratoire Atmospheres, Milieux, Observations Spatiales (LATMOS), IPSL, Paris, France
| | - Charles Miller
- NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California
| | - Michael Mischna
- NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California
| | - Michael Mumma
- NASA Goddard Space Flight Center, Greenbelt, Maryland
| | - Sally Newman
- California Institute of Technology, Pasadena, California
| | | | | | | | | | - Radu Popa
- University of Southern California, Los Angeles, California
| | - Michael Russell
- NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California
| | - Linhan Shen
- California Institute of Technology, Pasadena, California
| | | | - Robert Staehle
- NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California
| | - Vlada Stamenković
- California Institute of Technology, Pasadena, California
- NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California
| | | | | | - Ann C. Vandaele
- The Royal Belgian Institute for Space Aeronomy (BIRA-IASB), Brussels, Belgium
| | - Sébastien Viscardy
- The Royal Belgian Institute for Space Aeronomy (BIRA-IASB), Brussels, Belgium
| | - Christopher R. Webster
- NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California
| | | | | | - John Worden
- NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California
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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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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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Tokmina-Lukaszewska M, Patterson A, Berry L, Scott L, Balasubramanian N, Bothner B. The Role of Mass Spectrometry in Structural Studies of Flavin-Based Electron Bifurcating Enzymes. Front Microbiol 2018; 9:1397. [PMID: 30026733 PMCID: PMC6041385 DOI: 10.3389/fmicb.2018.01397] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2018] [Accepted: 06/07/2018] [Indexed: 12/01/2022] Open
Abstract
For decades, biologists and biochemists have taken advantage of atomic resolution structural models of proteins from X-ray crystallography, nuclear magnetic resonance spectroscopy, and more recently cryo-electron microscopy. However, not all proteins relent to structural analyses using these approaches, and as the depth of knowledge increases, additional data elucidating a mechanistic understanding of protein function is desired. Flavin-based electron bifurcating enzymes, which are responsible for producing high energy compounds through the simultaneous endergonic and exergonic reduction of two intercellular electron carriers (i.e., NAD+ and ferredoxin) are one class of proteins that have challenged structural biologists and in which there is great interest to understand the mechanism behind electron gating. A limited number of X-ray crystallography projects have been successful; however, it is clear that to understand how these enzymes function, techniques that can reveal detailed in solution information about protein structure, dynamics, and interactions involved in the bifurcating reaction are needed. In this review, we cover a general set of mass spectrometry-based techniques that, combined with protein modeling, are capable of providing information on both protein structure and dynamics. Techniques discussed include surface labeling, covalent cross-linking, native mass spectrometry, and hydrogen/deuterium exchange. We cover how biophysical data can be used to validate computationally generated protein models and develop mechanistic explanations for regulation and performance of enzymes and protein complexes. Our focus will be on flavin-based electron bifurcating enzymes, but the broad applicability of the techniques will be showcased.
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Affiliation(s)
| | - Angela Patterson
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, United States
| | - Luke Berry
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, United States
| | - Liam Scott
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, United States
| | | | - Brian Bothner
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, United States
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Baymann F, Schoepp-Cothenet B, Duval S, Guiral M, Brugna M, Baffert C, Russell MJ, Nitschke W. On the Natural History of Flavin-Based Electron Bifurcation. Front Microbiol 2018; 9:1357. [PMID: 30018596 PMCID: PMC6037941 DOI: 10.3389/fmicb.2018.01357] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 06/05/2018] [Indexed: 11/23/2022] Open
Abstract
Electron bifurcation is here described as a special case of the continuum of electron transfer reactions accessible to two-electron redox compounds with redox cooperativity. We argue that electron bifurcation is foremost an electrochemical phenomenon based on (a) strongly inverted redox potentials of the individual redox transitions, (b) a high endergonicity of the first redox transition, and (c) an escapement-type mechanism rendering completion of the first electron transfer contingent on occurrence of the second one. This mechanism is proposed to govern both the traditional quinone-based and the newly discovered flavin-based versions of electron bifurcation. Conserved and variable aspects of the spatial arrangement of electron transfer partners in flavoenzymes are assayed by comparing the presently available 3D structures. A wide sample of flavoenzymes is analyzed with respect to conserved structural modules and three major structural groups are identified which serve as basic frames for the evolutionary construction of a plethora of flavin-containing redox enzymes. We argue that flavin-based and other types of electron bifurcation are of primordial importance to free energy conversion, the quintessential foundation of life, and discuss a plausible evolutionary ancestry of the mechanism.
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Affiliation(s)
- Frauke Baymann
- CNRS, BIP, UMR 7281, IMM FR3479, Aix-Marseille University, Marseille, France
| | | | - Simon Duval
- CNRS, BIP, UMR 7281, IMM FR3479, Aix-Marseille University, Marseille, France
| | - Marianne Guiral
- CNRS, BIP, UMR 7281, IMM FR3479, Aix-Marseille University, Marseille, France
| | - Myriam Brugna
- CNRS, BIP, UMR 7281, IMM FR3479, Aix-Marseille University, Marseille, France
| | - Carole Baffert
- CNRS, BIP, UMR 7281, IMM FR3479, Aix-Marseille University, Marseille, France
| | - Michael J. Russell
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, United States
| | - Wolfgang Nitschke
- CNRS, BIP, UMR 7281, IMM FR3479, Aix-Marseille University, Marseille, France
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Yan Z, Ferry JG. Electron Bifurcation and Confurcation in Methanogenesis and Reverse Methanogenesis. Front Microbiol 2018; 9:1322. [PMID: 29973922 PMCID: PMC6019823 DOI: 10.3389/fmicb.2018.01322] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Accepted: 05/30/2018] [Indexed: 12/27/2022] Open
Abstract
Reduction of the disulfide of coenzyme M and coenzyme B (CoMS–SCoB) by heterodisulfide reductases (HdrED and HdrABC) is the final step in all methanogenic pathways. Flavin-based electron bifurcation (FBEB) by soluble HdrABC homologs play additional roles in driving essential endergonic reactions at the expense of the exergonic reduction of CoMS–SCoM. In the first step of the CO2 reduction pathway, HdrABC complexed with hydrogenase or formate dehydrogenase generates reduced ferredoxin (Fdx2-) for the endergonic reduction of CO2 coupled to the exergonic reduction of CoMS–SCoB dependent on FBEB of electrons from H2 or formate. Roles for HdrABC:hydrogenase complexes are also proposed for pathways wherein the methyl group of methanol is reduced to methane with electrons from H2. The HdrABC complexes catalyze FBEB-dependent oxidation of H2 for the endergonic reduction of Fdx driven by the exergonic reduction of CoMS–SCoB. The Fdx2- supplies electrons for reduction of the methyl group to methane. In H2- independent pathways, three-fourths of the methyl groups are oxidized producing Fdx2- and reduced coenzyme F420 (F420H2). The F420H2 donates electrons for reduction of the remaining methyl groups to methane requiring transfer of electrons from Fdx2- to F420. HdrA1B1C1 is proposed to catalyze FBEB-dependent oxidation of Fdx2- for the endergonic reduction of F420 driven by the exergonic reduction of CoMS–SCoB. In H2- independent acetotrophic pathways, the methyl group of acetate is reduced to methane with electrons derived from oxidation of the carbonyl group mediated by Fdx. Electron transport involves a membrane-bound complex (Rnf) that oxidizes Fdx2- and generates a Na+ gradient driving ATP synthesis. It is postulated that F420 is reduced by Rnf requiring HdrA2B2C2 catalyzing FBEB-dependent oxidation of F420H2 for the endergonic reduction of Fdx driven by the exergonic reduction of CoMS–SCoB. The Fdx2- is recycled by Rnf and HdrA2B2C2 thereby conserving energy. The HdrA2B2C2 is also proposed to play a role in Fe(III)-dependent reverse methanogenesis. A flavin-based electron confurcating (FBEC) HdrABC complex is proposed for nitrate-dependent reverse methanogenesis in which the oxidation of CoM-SH/CoB-SH and Fdx2- is coupled to reduction of F420. The F420H2 donates electrons to a membrane complex that generates a proton gradient driving ATP synthesis.
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Affiliation(s)
- Zhen Yan
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, State College, PA, United States
| | - James G Ferry
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, State College, PA, United States
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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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Martin WF, Bryant DA, Beatty JT. A physiological perspective on the origin and evolution of photosynthesis. FEMS Microbiol Rev 2018; 42:205-231. [PMID: 29177446 PMCID: PMC5972617 DOI: 10.1093/femsre/fux056] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 11/20/2017] [Indexed: 12/22/2022] Open
Abstract
The origin and early evolution of photosynthesis are reviewed from an ecophysiological perspective. Earth's first ecosystems were chemotrophic, fueled by geological H2 at hydrothermal vents and, required flavin-based electron bifurcation to reduce ferredoxin for CO2 fixation. Chlorophyll-based phototrophy (chlorophototrophy) allowed autotrophs to generate reduced ferredoxin without electron bifurcation, providing them access to reductants other than H2. Because high-intensity, short-wavelength electromagnetic radiation at Earth's surface would have been damaging for the first chlorophyll (Chl)-containing cells, photosynthesis probably arose at hydrothermal vents under low-intensity, long-wavelength geothermal light. The first photochemically active pigments were possibly Zn-tetrapyrroles. We suggest that (i) after the evolution of red-absorbing Chl-like pigments, the first light-driven electron transport chains reduced ferredoxin via a type-1 reaction center (RC) progenitor with electrons from H2S; (ii) photothioautotrophy, first with one RC and then with two, was the bridge between H2-dependent chemolithoautotrophy and water-splitting photosynthesis; (iii) photothiotrophy sustained primary production in the photic zone of Archean oceans; (iv) photosynthesis arose in an anoxygenic cyanobacterial progenitor; (v) Chl a is the ancestral Chl; and (vi), anoxygenic chlorophototrophic lineages characterized so far acquired, by horizontal gene transfer, RCs and Chl biosynthesis with or without autotrophy, from the architects of chlorophototrophy-the cyanobacterial lineage.
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Affiliation(s)
- William F Martin
- Institute for Molecular Evolution, University of Düsseldorf, D-40225 Düsseldorf, Germany
| | - Donald A Bryant
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, USA
| | - J Thomas Beatty
- Department of Microbiology and Immunology, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC, V6T 1Z3, Canada
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75
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Duan HD, Lubner CE, Tokmina-Lukaszewska M, Gauss GH, Bothner B, King PW, Peters JW, Miller AF. Distinct properties underlie flavin-based electron bifurcation in a novel electron transfer flavoprotein FixAB from Rhodopseudomonas palustris. J Biol Chem 2018; 293:4688-4701. [PMID: 29462786 DOI: 10.1074/jbc.ra117.000707] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Revised: 02/08/2018] [Indexed: 11/06/2022] Open
Abstract
A newly recognized third fundamental mechanism of energy conservation in biology, electron bifurcation, uses free energy from exergonic redox reactions to drive endergonic redox reactions. Flavin-based electron bifurcation furnishes low-potential electrons to demanding chemical reactions, such as reduction of dinitrogen to ammonia. We employed the heterodimeric flavoenzyme FixAB from the diazotrophic bacterium Rhodopseudomonas palustris to elucidate unique properties that underpin flavin-based electron bifurcation. FixAB is distinguished from canonical electron transfer flavoproteins (ETFs) by a second FAD that replaces the AMP of canonical ETF. We exploited near-UV-visible CD spectroscopy to resolve signals from the different flavin sites in FixAB and to interrogate the putative bifurcating FAD. CD aided in assigning the measured reduction midpoint potentials (E° values) to individual flavins, and the E° values tested the accepted model regarding the redox properties required for bifurcation. We found that the higher-E° flavin displays sequential one-electron (1-e-) reductions to anionic semiquinone and then to hydroquinone, consistent with the reactivity seen in canonical ETFs. In contrast, the lower-E° flavin displayed a single two-electron (2-e-) reduction without detectable accumulation of semiquinone, consistent with unstable semiquinone states, as required for bifurcation. This is the first demonstration that a FixAB protein possesses the thermodynamic prerequisites for bifurcating activity, and the separation of distinct optical signatures for the two flavins lays a foundation for mechanistic studies to learn how electron flow can be directed in a protein environment. We propose that a novel optical signal observed at long wavelength may reflect electron delocalization between the two flavins.
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Affiliation(s)
- H Diessel Duan
- Department of Chemistry, University of Kentucky, Lexington, Kentucky 40506
| | | | | | - George H Gauss
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717
| | - Brian Bothner
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717
| | - Paul W King
- National Renewable Energy Laboratory, Golden, Colorado 80401
| | - John W Peters
- Institute of Biological Chemistry, Washington State University, Pullman, Washington 99163
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76
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Molecular basis of the flavin-based electron-bifurcating caffeyl-CoA reductase reaction. FEBS Lett 2018; 592:332-342. [DOI: 10.1002/1873-3468.12971] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Revised: 01/04/2018] [Accepted: 01/04/2018] [Indexed: 11/07/2022]
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77
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Sousa FL, Preiner M, Martin WF. Native metals, electron bifurcation, and CO 2 reduction in early biochemical evolution. Curr Opin Microbiol 2018; 43:77-83. [PMID: 29316496 DOI: 10.1016/j.mib.2017.12.010] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Revised: 12/21/2017] [Accepted: 12/22/2017] [Indexed: 12/22/2022]
Abstract
Molecular hydrogen is an ancient source of energy and electrons. Anaerobic autotrophs that harness the H2/CO2 redox couple harbour ancient biochemical traits that trace back to the universal common ancestor. Aspects of their physiology, including the abundance of transition metals, radical reaction mechanisms, and their main exergonic bioenergetic reactions, forge links between ancient microbes and geochemical reactions at hydrothermal vents. The midpoint potential of H2 however requires anaerobes that reduce CO2 with H2 to use flavin based electron bifurcation-a mechanism to conserve energy as low potential reduced ferredoxins via soluble proteins-for CO2 fixation. This presents a paradox. At the onset of biochemical evolution, before there were proteins, how was CO2 reduced using H2? FeS minerals alone are probably not the solution, because biological CO2 reduction is a two electron reaction. Physiology can provide clues. Some acetogens and some methanogens can grow using native iron (Fe0) instead of H2 as the electron donor. In the laboratory, Fe0 efficiently reduces CO2 to acetate and methanol. Hydrothermal vents harbour awaruite, Ni3Fe, a natural compound of native metals. Native metals might have been the precursors of electron bifurcation in biochemical evolution.
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Affiliation(s)
- Filipa L Sousa
- Division of Archaea Biology and Ecogenomics, Department of Ecogenomics and Systems Biology, University of Vienna, Althanstrasse 14 UZA I, 1090 Vienna, Austria.
| | - Martina Preiner
- Institute of Molecular Evolution, Heinrich-Heine-University, Universitätsstr. 1, 40225 Düsseldorf, Germany
| | - William F Martin
- Institute of Molecular Evolution, Heinrich-Heine-University, Universitätsstr. 1, 40225 Düsseldorf, Germany; Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, 2780-157 Oeiras, Portugal
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78
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Berry L, Patterson A, Pence N, Peters JW, Bothner B. Hydrogen Deuterium Exchange Mass Spectrometry of Oxygen Sensitive Proteins. Bio Protoc 2018; 8:e2769. [PMID: 29713655 DOI: 10.21769/bioprotoc.2769] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
Abstract
The protocol detailed here describes a way to perform hydrogen deuterium exchange coupled to mass spectrometry (HDX-MS) on oxygen sensitive proteins. HDX-MS is a powerful tool for studying the protein structure-function relationship. Applying this technique to anaerobic proteins provides insight into the mechanism of proteins that perform oxygen sensitive chemistry. A problem when using HDX-MS to study anaerobic proteins is that there are many parts that require constant movement into and out of an anaerobic chamber. This can affect the seal, increasing the likelihood of oxygen exposure. Exposure to oxygen causes the cofactors bound to these proteins, a common example being FeS clusters, to no longer interact with the amino acid residues responsible for coordinating the FeS clusters, causing loss of the clusters and irreversible inactivation of the protein. To counteract this, a double vial system was developed that allows the preparation of solutions and reaction mixtures anaerobically, but also allows these solutions to be moved to an aerobic environment while shielding the solutions from oxygen. Additionally, movement isn't limited like it is in an anaerobic chamber, ensuring more consistent data, and fewer errors during the course of the reaction.
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Affiliation(s)
- Luke Berry
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, USA
| | - Angela Patterson
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, USA
| | - Natasha Pence
- Institute of Biological Chemistry, Washington State University, Pullman, USA
| | - John W Peters
- Institute of Biological Chemistry, Washington State University, Pullman, USA
| | - Brian Bothner
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, USA
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79
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Peters JW, Beratan DN, Schut GJ, Adams MWW. On the nature of organic and inorganic centers that bifurcate electrons, coupling exergonic and endergonic oxidation–reduction reactions. Chem Commun (Camb) 2018; 54:4091-4099. [DOI: 10.1039/c8cc01530a] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Bifurcating electrons to couple endergonic and exergonic electron-transfer reactions has been shown to have a key role in energy conserving redox enzymes.
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Affiliation(s)
- John W. Peters
- Institute of Biological Chemistry, Washington State University
- Pullman
- USA
| | - David N. Beratan
- Department of Chemistry and Department of Physics, Duke University
- Durham
- USA
- Department of Biochemistry, Duke University
- Durham
| | - Gerrit J. Schut
- Department of Biochemistry and Molecular Biology, University of Georgia
- Athens
- USA
| | - Michael W. W. Adams
- Department of Biochemistry and Molecular Biology, University of Georgia
- Athens
- USA
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80
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Homoacetogenesis in Deep-Sea Chloroflexi, as Inferred by Single-Cell Genomics, Provides a Link to Reductive Dehalogenation in Terrestrial Dehalococcoidetes. mBio 2017; 8:mBio.02022-17. [PMID: 29259088 PMCID: PMC5736913 DOI: 10.1128/mbio.02022-17] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
The deep marine subsurface is one of the largest unexplored biospheres on Earth and is widely inhabited by members of the phylum Chloroflexi. In this report, we investigated genomes of single cells obtained from deep-sea sediments of the Peruvian Margin, which are enriched in such Chloroflexi. 16S rRNA gene sequence analysis placed two of these single-cell-derived genomes (DscP3 and Dsc4) in a clade of subphylum I Chloroflexi which were previously recovered from deep-sea sediment in the Okinawa Trough and a third (DscP2-2) as a member of the previously reported DscP2 population from Peruvian Margin site 1230. The presence of genes encoding enzymes of a complete Wood-Ljungdahl pathway, glycolysis/gluconeogenesis, a Rhodobacter nitrogen fixation (Rnf) complex, glyosyltransferases, and formate dehydrogenases in the single-cell genomes of DscP3 and Dsc4 and the presence of an NADH-dependent reduced ferredoxin:NADP oxidoreductase (Nfn) and Rnf in the genome of DscP2-2 imply a homoacetogenic lifestyle of these abundant marine Chloroflexi. We also report here the first complete pathway for anaerobic benzoate oxidation to acetyl coenzyme A (CoA) in the phylum Chloroflexi (DscP3 and Dsc4), including a class I benzoyl-CoA reductase. Of remarkable evolutionary significance, we discovered a gene encoding a formate dehydrogenase (FdnI) with reciprocal closest identity to the formate dehydrogenase-like protein (complex iron-sulfur molybdoenzyme [CISM], DET0187) of terrestrial Dehalococcoides/Dehalogenimonas spp. This formate dehydrogenase-like protein has been shown to lack formate dehydrogenase activity in Dehalococcoides/Dehalogenimonas spp. and is instead hypothesized to couple HupL hydrogenase to a reductive dehalogenase in the catabolic reductive dehalogenation pathway. This finding of a close functional homologue provides an important missing link for understanding the origin and the metabolic core of terrestrial Dehalococcoides/Dehalogenimonas spp. and of reductive dehalogenation, as well as the biology of abundant deep-sea Chloroflexi. The deep marine subsurface is one of the largest unexplored biospheres on Earth and is widely inhabited by members of the phylum Chloroflexi. In this report, we investigated genomes of single cells obtained from deep-sea sediments and provide evidence for a homacetogenic lifestyle of these abundant marine Chloroflexi. Moreover, genome signature and key metabolic genes indicate an evolutionary relationship between these deep-sea sediment microbes and terrestrial, reductively dehalogenating Dehalococcoides.
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81
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Demmer JK, Pal Chowdhury N, Selmer T, Ermler U, Buckel W. The semiquinone swing in the bifurcating electron transferring flavoprotein/butyryl-CoA dehydrogenase complex from Clostridium difficile. Nat Commun 2017; 8:1577. [PMID: 29146947 PMCID: PMC5691135 DOI: 10.1038/s41467-017-01746-3] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 10/13/2017] [Indexed: 11/29/2022] Open
Abstract
The electron transferring flavoprotein/butyryl-CoA dehydrogenase (EtfAB/Bcd) catalyzes the reduction of one crotonyl-CoA and two ferredoxins by two NADH within a flavin-based electron-bifurcating process. Here we report on the X-ray structure of the Clostridium difficile (EtfAB/Bcd)4 complex in the dehydrogenase-conducting D-state, α-FAD (bound to domain II of EtfA) and δ-FAD (bound to Bcd) being 8 Å apart. Superimposing Acidaminococcus fermentans EtfAB onto C. difficile EtfAB/Bcd reveals a rotation of domain II of nearly 80°. Further rotation by 10° brings EtfAB into the bifurcating B-state, α-FAD and β-FAD (bound to EtfB) being 14 Å apart. This dual binding mode of domain II, substantiated by mutational studies, resembles findings in non-bifurcating EtfAB/acyl-CoA dehydrogenase complexes. In our proposed mechanism, NADH reduces β-FAD, which bifurcates. One electron goes to ferredoxin and one to α-FAD, which swings over to reduce δ-FAD to the semiquinone. Repetition affords a second reduced ferredoxin and δ-FADH−, which reduces crotonyl-CoA. The electron-transferring flavoprotein / butyryl-CoA dehydrogenase (EtfAB/Bcd) complex catalyzes the reduction of crotonyl-CoA and ferredoxins by NADH in anaerobic microbes. Here, the authors present the crystal structure of Clostridium difficile EtfAB/Bcd and discuss the bifurcation mechanism for electron flow.
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Affiliation(s)
- Julius K Demmer
- Max-Planck-Institut für Biophysik, Max-von-Laue-Str. 3, 60438, Frankfurt am Main, Germany
| | - Nilanjan Pal Chowdhury
- 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
| | - Thorsten Selmer
- Fachbereich Chemie und Biotechnologie, FH Aachen, Heinrich-Mußmann-Str. 1, 52428, Jülich, Germany
| | - Ulrich Ermler
- Max-Planck-Institut für Biophysik, Max-von-Laue-Str. 3, 60438, Frankfurt am Main, 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.
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82
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Lubner CE, Peters JW. Electron Bifurcation Makes the Puzzle Pieces Fall Energetically into Place in Methanogenic Energy Conservation. Chembiochem 2017; 18:2295-2297. [PMID: 28986941 DOI: 10.1002/cbic.201700533] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Indexed: 12/25/2022]
Abstract
Elaborate arrays of iron-sulfur clusters link active sites via a flavin that bifurcates electrons through two energetically independent paths. The structure of the heterodisulfide reductase provides insight into how methanogens conserve energy through coupling hydrogen oxidation to coordinated exergonic heterodisulfide and endergonic ferredoxin reduction in an overall thermodynamically favorable reaction.
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Affiliation(s)
- Carolyn E Lubner
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver W Parkway, Golden, CO, 80401, USA
| | - John W Peters
- Institute of Biological Chemistry, Washington State University, Pullman, WA, 99164, USA
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83
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Losey NA, Mus F, Peters JW, Le HM, McInerney MJ. Syntrophomonas wolfei Uses an NADH-Dependent, Ferredoxin-Independent [FeFe]-Hydrogenase To Reoxidize NADH. Appl Environ Microbiol 2017; 83:e01335-17. [PMID: 28802265 PMCID: PMC5626996 DOI: 10.1128/aem.01335-17] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Accepted: 07/29/2017] [Indexed: 12/19/2022] Open
Abstract
Syntrophomonas wolfei syntrophically oxidizes short-chain fatty acids (four to eight carbons in length) when grown in coculture with a hydrogen- and/or formate-using methanogen. The oxidation of 3-hydroxybutyryl-coenzyme A (CoA), formed during butyrate metabolism, results in the production of NADH. The enzyme systems involved in NADH reoxidation in S. wolfei are not well understood. The genome of S. wolfei contains a multimeric [FeFe]-hydrogenase that may be a mechanism for NADH reoxidation. The S. wolfei genes for the multimeric [FeFe]-hydrogenase (hyd1ABC; SWOL_RS05165, SWOL_RS05170, SWOL_RS05175) and [FeFe]-hydrogenase maturation proteins (SWOL_RS05180, SWOL_RS05190, SWOL_RS01625) were coexpressed in Escherichia coli, and the recombinant Hyd1ABC was purified and characterized. The purified recombinant Hyd1ABC was a heterotrimer with an αβγ configuration and a molecular mass of 115 kDa. Hyd1ABC contained 29.2 ± 1.49 mol of Fe and 0.7 mol of flavin mononucleotide (FMN) per mole enzyme. The purified, recombinant Hyd1ABC reduced NAD+ and oxidized NADH without the presence of ferredoxin. The HydB subunit of the S. wolfei multimeric [FeFe]-hydrogenase lacks two iron-sulfur centers that are present in known confurcating NADH- and ferredoxin-dependent [FeFe]-hydrogenases. Hyd1ABC is a NADH-dependent hydrogenase that produces hydrogen from NADH without the need of reduced ferredoxin, which differs from confurcating [FeFe]-hydrogenases. Hyd1ABC provides a mechanism by which S. wolfei can reoxidize NADH produced during syntrophic butyrate oxidation when low hydrogen partial pressures are maintained by a hydrogen-consuming microorganism.IMPORTANCE Our work provides mechanistic understanding of the obligate metabolic coupling that occurs between hydrogen-producing fatty and aromatic acid-degrading microorganisms and their hydrogen-consuming partners in the process called syntrophy (feeding together). The multimeric [FeFe]-hydrogenase used NADH without the involvement of reduced ferredoxin. The multimeric [FeFe]-hydrogenase would produce hydrogen from NADH only when hydrogen concentrations were low. Hydrogen production from NADH by Syntrophomonas wolfei would likely cease before any detectable amount of cell growth occurred. Thus, continual hydrogen production requires the presence of a hydrogen-consuming partner to keep hydrogen concentrations low and explains, in part, the obligate requirement that S. wolfei has for a hydrogen-consuming partner organism during growth on butyrate. We have successfully expressed genes encoding a multimeric [FeFe]-hydrogenase in E. coli, demonstrating that such an approach can be advantageous to characterize complex redox proteins from difficult-to-culture microorganisms.
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Affiliation(s)
- Nathaniel A Losey
- Department of Plant Biology and Microbiology, University of Oklahoma, Norman, Oklahoma, USA
| | - Florence Mus
- Department of Chemistry and Biochemistry, Institute of Biological Chemistry, Washington State University, Pullman, Washington, USA
| | - John W Peters
- Department of Chemistry and Biochemistry, Institute of Biological Chemistry, Washington State University, Pullman, Washington, USA
| | - Huynh M Le
- Department of Plant Biology and Microbiology, University of Oklahoma, Norman, Oklahoma, USA
| | - Michael J McInerney
- Department of Plant Biology and Microbiology, University of Oklahoma, Norman, Oklahoma, USA
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84
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Berry L, Poudel S, Tokmina-Lukaszewska M, Colman DR, Nguyen DMN, Schut GJ, Adams MWW, Peters JW, Boyd ES, Bothner B. H/D exchange mass spectrometry and statistical coupling analysis reveal a role for allostery in a ferredoxin-dependent bifurcating transhydrogenase catalytic cycle. Biochim Biophys Acta Gen Subj 2017; 1862:9-17. [PMID: 28993252 DOI: 10.1016/j.bbagen.2017.10.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Revised: 09/26/2017] [Accepted: 10/05/2017] [Indexed: 10/18/2022]
Abstract
Recent investigations into ferredoxin-dependent transhydrogenases, a class of enzymes responsible for electron transport, have highlighted the biological importance of flavin-based electron bifurcation (FBEB). FBEB generates biomolecules with very low reduction potential by coupling the oxidation of an electron donor with intermediate potential to the reduction of high and low potential molecules. Bifurcating systems can generate biomolecules with very low reduction potentials, such as reduced ferredoxin (Fd), from species such as NADPH. Metabolic systems that use bifurcation are more efficient and confer a competitive advantage for the organisms that harbor them. Structural models are now available for two NADH-dependent ferredoxin-NADP+ oxidoreductase (Nfn) complexes. These models, together with spectroscopic studies, have provided considerable insight into the catalytic process of FBEB. However, much about the mechanism and regulation of these multi-subunit proteins remains unclear. Using hydrogen/deuterium exchange mass spectrometry (HDX-MS) and statistical coupling analysis (SCA), we identified specific pathways of communication within the model FBEB system, Nfn from Pyrococus furiosus, under conditions at each step of the catalytic cycle. HDX-MS revealed evidence for allosteric coupling across protein subunits upon nucleotide and ferredoxin binding. SCA uncovered a network of co-evolving residues that can provide connectivity across the complex. Together, the HDX-MS and SCA data show that protein allostery occurs across the ensemble of iron‑sulfur cofactors and ligand binding sites using specific pathways that connect domains allowing them to function as dynamically coordinated units.
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Affiliation(s)
- Luke Berry
- Montana State University, Bozeman, MT 59717, United States.
| | - Saroj Poudel
- Montana State University, Bozeman, MT 59717, United States.
| | | | | | | | | | | | - John W Peters
- Washington State University, Pullman, WA, United States.
| | - Eric S Boyd
- Montana State University, Bozeman, MT 59717, United States.
| | - Brian Bothner
- Montana State University, Bozeman, MT 59717, United States.
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85
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Defining Electron Bifurcation in the Electron-Transferring Flavoprotein Family. J Bacteriol 2017; 199:JB.00440-17. [PMID: 28808132 DOI: 10.1128/jb.00440-17] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Accepted: 08/09/2017] [Indexed: 11/20/2022] Open
Abstract
Electron bifurcation is the coupling of exergonic and endergonic redox reactions to simultaneously generate (or utilize) low- and high-potential electrons. It is the third recognized form of energy conservation in biology and was recently described for select electron-transferring flavoproteins (Etfs). Etfs are flavin-containing heterodimers best known for donating electrons derived from fatty acid and amino acid oxidation to an electron transfer respiratory chain via Etf-quinone oxidoreductase. Canonical examples contain a flavin adenine dinucleotide (FAD) that is involved in electron transfer, as well as a non-redox-active AMP. However, Etfs demonstrated to bifurcate electrons contain a second FAD in place of the AMP. To expand our understanding of the functional variety and metabolic significance of Etfs and to identify amino acid sequence motifs that potentially enable electron bifurcation, we compiled 1,314 Etf protein sequences from genome sequence databases and subjected them to informatic and structural analyses. Etfs were identified in diverse archaea and bacteria, and they clustered into five distinct well-supported groups, based on their amino acid sequences. Gene neighborhood analyses indicated that these Etf group designations largely correspond to putative differences in functionality. Etfs with the demonstrated ability to bifurcate were found to form one group, suggesting that distinct conserved amino acid sequence motifs enable this capability. Indeed, structural modeling and sequence alignments revealed that identifying residues occur in the NADH- and FAD-binding regions of bifurcating Etfs. Collectively, a new classification scheme for Etf proteins that delineates putative bifurcating versus nonbifurcating members is presented and suggests that Etf-mediated bifurcation is associated with surprisingly diverse enzymes.IMPORTANCE Electron bifurcation has recently been recognized as an electron transfer mechanism used by microorganisms to maximize energy conservation. Bifurcating enzymes couple thermodynamically unfavorable reactions with thermodynamically favorable reactions in an overall spontaneous process. Here we show that the electron-transferring flavoprotein (Etf) enzyme family exhibits far greater diversity than previously recognized, and we provide a phylogenetic analysis that clearly delineates bifurcating versus nonbifurcating members of this family. Structural modeling of proteins within these groups reveals key differences between the bifurcating and nonbifurcating Etfs.
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86
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Structure and electrochemistry of proteins harboring iron-sulfur clusters of different nuclearities. Part I. [4Fe-4S] + [2Fe-2S] iron-sulfur proteins. J Struct Biol 2017; 200:1-19. [DOI: 10.1016/j.jsb.2017.05.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Accepted: 05/25/2017] [Indexed: 01/08/2023]
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87
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Zhang P, Yuly JL, Lubner CE, Mulder DW, King PW, Peters JW, Beratan DN. Electron Bifurcation: Thermodynamics and Kinetics of Two-Electron Brokering in Biological Redox Chemistry. Acc Chem Res 2017; 50:2410-2417. [PMID: 28876046 DOI: 10.1021/acs.accounts.7b00327] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
How can proteins drive two electrons from a redox active donor onto two acceptors at very different potentials and distances? And how can this transaction be conducted without dissipating very much energy or violating the laws of thermodynamics? Nature appears to have addressed these challenges by coupling thermodynamically uphill and downhill electron transfer reactions, using two-electron donor cofactors that have very different potentials for the removal of the first and second electron. Although electron bifurcation is carried out with near perfection from the standpoint of energy conservation and electron delivery yields, it is a biological energy transduction paradigm that has only come into focus recently. This Account provides an exegesis of the biophysical principles that underpin electron bifurcation. Remarkably, bifurcating electron transfer (ET) proteins typically send one electron uphill and one electron downhill by similar energies, such that the overall reaction is spontaneous, but not profligate. Electron bifurcation in the NADH-dependent reduced ferredoxin: NADP+ oxidoreductase I (Nfn) is explored in detail here. Recent experimental progress in understanding the structure and function of Nfn allows us to dissect its workings in the framework of modern ET theory. The first electron that leaves the two-electron donor flavin (L-FAD) executes a positive free energy "uphill" reaction, and the departure of this electron switches on a second thermodynamically spontaneous ET reaction from the flavin along a second pathway that moves electrons in the opposite direction and at a very different potential. The singly reduced ET products formed from the bifurcating flavin are more than two nanometers distant from each other. In Nfn, the second electron to leave the flavin is much more reducing than the first: the potentials are said to be "crossed." The eventually reduced cofactors, NADH and ferredoxin in the case of Nfn, perform crucial downstream redox processes of their own. We dissect the thermodynamics and kinetics of electron bifurcation in Nfn and find that the key features of electron bifurcation are (1) spatially separated transfer pathways that diverge from a two-electron donor, (2) one thermodynamically uphill and one downhill redox pathway, with a large negative shift in the donor's reduction potential after departure of the first electron, and (3) electron tunneling and activation factors that enable bifurcation, producing a 1:1 partitioning of electrons onto the two pathways. Electron bifurcation is found in the CO2 reducing pathways of methanogenic archaea, in the hydrogen pathways of hydrogenases, in the nitrogen fixing pathway of Fix, and in the mitochondrial charge transfer chain of complex III, cytochrome bc1. While crossed potentials may offer the biological advantage of producing tightly regulated high energy reactive species, neither kinetic nor thermodynamic considerations mandate crossed potentials to generate successful electron bifurcation. Taken together, the theoretical framework established here, focusing on the underpinning electron tunneling barriers and activation free energies, explains the logic of electron bifurcation that enables energy conversion and conservation in Nfn, points toward bioinspired schemes to execute multielectron redox chemistry, and establishes a roadmap for examining novel electron bifurcation networks in nature.
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Affiliation(s)
| | | | - Carolyn E. Lubner
- National Renewable Energy Laboratory, Golden, Colorado 80401, United States
| | - David W. Mulder
- National Renewable Energy Laboratory, Golden, Colorado 80401, United States
| | - Paul W. King
- National Renewable Energy Laboratory, Golden, Colorado 80401, United States
| | - John W. Peters
- Institute
of Biological Chemistry, Washington State University, Pullman, Washington 99163, United States
| | - David N. Beratan
- Department
of Biochemistry, Duke University, Durham, North Carolina 27710, United States
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88
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Ledbetter RN, Garcia Costas AM, Lubner CE, Mulder DW, Tokmina-Lukaszewska M, Artz JH, Patterson A, Magnuson TS, Jay ZJ, Duan HD, Miller J, Plunkett MH, Hoben JP, Barney BM, Carlson RP, Miller AF, Bothner B, King PW, Peters JW, Seefeldt LC. The Electron Bifurcating FixABCX Protein Complex from Azotobacter vinelandii: Generation of Low-Potential Reducing Equivalents for Nitrogenase Catalysis. Biochemistry 2017; 56:4177-4190. [PMID: 28704608 DOI: 10.1021/acs.biochem.7b00389] [Citation(s) in RCA: 98] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The biological reduction of dinitrogen (N2) to ammonia (NH3) by nitrogenase is an energetically demanding reaction that requires low-potential electrons and ATP; however, pathways used to deliver the electrons from central metabolism to the reductants of nitrogenase, ferredoxin or flavodoxin, remain unknown for many diazotrophic microbes. The FixABCX protein complex has been proposed to reduce flavodoxin or ferredoxin using NADH as the electron donor in a process known as electron bifurcation. Herein, the FixABCX complex from Azotobacter vinelandii was purified and demonstrated to catalyze an electron bifurcation reaction: oxidation of NADH (Em = -320 mV) coupled to reduction of flavodoxin semiquinone (Em = -460 mV) and reduction of coenzyme Q (Em = 10 mV). Knocking out fix genes rendered Δrnf A. vinelandii cells unable to fix dinitrogen, confirming that the FixABCX system provides another route for delivery of electrons to nitrogenase. Characterization of the purified FixABCX complex revealed the presence of flavin and iron-sulfur cofactors confirmed by native mass spectrometry, electron paramagnetic resonance spectroscopy, and transient absorption spectroscopy. Transient absorption spectroscopy further established the presence of a short-lived flavin semiquinone radical, suggesting that a thermodynamically unstable flavin semiquinone may participate as an intermediate in the transfer of an electron to flavodoxin. A structural model of FixABCX, generated using chemical cross-linking in conjunction with homology modeling, revealed plausible electron transfer pathways to both high- and low-potential acceptors. Overall, this study informs a mechanism for electron bifurcation, offering insight into a unique method for delivery of low-potential electrons required for energy-intensive biochemical conversions.
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Affiliation(s)
- Rhesa N Ledbetter
- Department of Chemistry and Biochemistry, Utah State University , Logan, Utah 84322, United States
| | - Amaya M Garcia Costas
- Department of Chemistry and Biochemistry, Montana State University , Bozeman, Montana 59717, United States
| | - Carolyn E Lubner
- National Renewable Energy Laboratory , Golden, Colorado 80401, United States
| | - David W Mulder
- National Renewable Energy Laboratory , Golden, Colorado 80401, United States
| | - Monika Tokmina-Lukaszewska
- Department of Chemistry and Biochemistry, Montana State University , Bozeman, Montana 59717, United States
| | - Jacob H Artz
- Institute of Biological Chemistry, Washington State University , Pullman, Washington 99163, United States
| | - Angela Patterson
- Department of Chemistry and Biochemistry, Montana State University , Bozeman, Montana 59717, United States
| | - Timothy S Magnuson
- Department of Biological Sciences, Idaho State University , Pocatello, Idaho 83201, United States
| | - Zackary J Jay
- Department of Chemical and Biological Engineering, Center for Biofilm Engineering and Thermal Biology Institute, Montana State University , Bozeman, Montana 59717, United States
| | - H Diessel Duan
- Department of Chemistry, University of Kentucky , Lexington, Kentucky 40506, United States
| | - Jacquelyn Miller
- Department of Chemistry and Biochemistry, Montana State University , Bozeman, Montana 59717, United States
| | - Mary H Plunkett
- Department of Bioproducts and Biosystems Engineering and Biotechnology Institute, University of Minnesota , St. Paul, Minnesota 55108, United States
| | - John P Hoben
- Department of Chemistry, University of Kentucky , Lexington, Kentucky 40506, United States
| | - Brett M Barney
- Department of Bioproducts and Biosystems Engineering and Biotechnology Institute, University of Minnesota , St. Paul, Minnesota 55108, United States
| | - Ross P Carlson
- Department of Chemical and Biological Engineering, Center for Biofilm Engineering and Thermal Biology Institute, Montana State University , Bozeman, Montana 59717, United States
| | - Anne-Frances Miller
- Department of Chemistry, University of Kentucky , Lexington, Kentucky 40506, United States
| | - Brian Bothner
- Department of Chemistry and Biochemistry, Montana State University , Bozeman, Montana 59717, United States
| | - Paul W King
- National Renewable Energy Laboratory , Golden, Colorado 80401, United States
| | - John W Peters
- Department of Chemistry and Biochemistry, Montana State University , Bozeman, Montana 59717, United States.,Institute of Biological Chemistry, Washington State University , Pullman, Washington 99163, United States
| | - Lance C Seefeldt
- Department of Chemistry and Biochemistry, Utah State University , Logan, Utah 84322, United States
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89
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Nguyen DMN, Schut GJ, Zadvornyy OA, Tokmina-Lukaszewska M, Poudel S, Lipscomb GL, Adams LA, Dinsmore JT, Nixon WJ, Boyd ES, Bothner B, Peters JW, Adams MWW. Two functionally distinct NADP +-dependent ferredoxin oxidoreductases maintain the primary redox balance of Pyrococcus furiosus. J Biol Chem 2017; 292:14603-14616. [PMID: 28705933 DOI: 10.1074/jbc.m117.794172] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Revised: 07/10/2017] [Indexed: 01/08/2023] Open
Abstract
Electron bifurcation has recently gained acceptance as the third mechanism of energy conservation in which energy is conserved through the coupling of exergonic and endergonic reactions. A structure-based mechanism of bifurcation has been elucidated recently for the flavin-based enzyme NADH-dependent ferredoxin NADP+ oxidoreductase I (NfnI) from the hyperthermophillic archaeon Pyrococcus furiosus. NfnI is thought to be involved in maintaining the cellular redox balance, producing NADPH for biosynthesis by recycling the two other primary redox carriers, NADH and ferredoxin. The P. furiosus genome encodes an NfnI paralog termed NfnII, and the two are differentially expressed, depending on the growth conditions. In this study, we show that deletion of the genes encoding either NfnI or NfnII affects the cellular concentrations of NAD(P)H and particularly NADPH. This results in a moderate to severe growth phenotype in deletion mutants, demonstrating a key role for each enzyme in maintaining redox homeostasis. Despite their similarity in primary sequence and cofactor content, crystallographic, kinetic, and mass spectrometry analyses reveal that there are fundamental structural differences between the two enzymes, and NfnII does not catalyze the NfnI bifurcating reaction. Instead, it exhibits non-bifurcating ferredoxin NADP oxidoreductase-type activity. NfnII is therefore proposed to be a bifunctional enzyme and also to catalyze a bifurcating reaction, although its third substrate, in addition to ferredoxin and NADP(H), is as yet unknown.
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Affiliation(s)
- Diep M N Nguyen
- From the Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602
| | - Gerrit J Schut
- From the Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602
| | - Oleg A Zadvornyy
- the Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164, and
| | | | - Saroj Poudel
- Microbiology and Immunology, Montana State University, Bozeman, Montana 59717
| | - Gina L Lipscomb
- From the Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602
| | - Leslie A Adams
- From the Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602
| | - Jessica T Dinsmore
- From the Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602
| | - William J Nixon
- From the Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602
| | - Eric S Boyd
- Microbiology and Immunology, Montana State University, Bozeman, Montana 59717
| | | | - John W Peters
- the Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164, and
| | - Michael W W Adams
- From the Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602,
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90
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Hoben JP, Lubner CE, Ratzloff MW, Schut GJ, Nguyen DMN, Hempel KW, Adams MWW, King PW, Miller AF. Equilibrium and ultrafast kinetic studies manipulating electron transfer: A short-lived flavin semiquinone is not sufficient for electron bifurcation. J Biol Chem 2017; 292:14039-14049. [PMID: 28615449 DOI: 10.1074/jbc.m117.794214] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Revised: 06/11/2017] [Indexed: 11/06/2022] Open
Abstract
Flavin-based electron transfer bifurcation is emerging as a fundamental and powerful mechanism for conservation and deployment of electrochemical energy in enzymatic systems. In this process, a pair of electrons is acquired at intermediate reduction potential (i.e. intermediate reducing power), and each electron is passed to a different acceptor, one with lower and the other with higher reducing power, leading to "bifurcation." It is believed that a strongly reducing semiquinone species is essential for this process, and it is expected that this species should be kinetically short-lived. We now demonstrate that the presence of a short-lived anionic flavin semiquinone (ASQ) is not sufficient to infer the existence of bifurcating activity, although such a species may be necessary for the process. We have used transient absorption spectroscopy to compare the rates and mechanisms of decay of ASQ generated photochemically in bifurcating NADH-dependent ferredoxin-NADP+ oxidoreductase and the non-bifurcating flavoproteins nitroreductase, NADH oxidase, and flavodoxin. We found that different mechanisms dominate ASQ decay in the different protein environments, producing lifetimes ranging over 2 orders of magnitude. Capacity for electron transfer among redox cofactors versus charge recombination with nearby donors can explain the range of ASQ lifetimes that we observe. Our results support a model wherein efficient electron propagation can explain the short lifetime of the ASQ of bifurcating NADH-dependent ferredoxin-NADP+ oxidoreductase I and can be an indication of capacity for electron bifurcation.
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Affiliation(s)
- John P Hoben
- From the Department of Chemistry, University of Kentucky, Lexington, Kentucky 40506
| | | | | | - Gerrit J Schut
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602
| | - Diep M N Nguyen
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602
| | - Karl W Hempel
- From the Department of Chemistry, University of Kentucky, Lexington, Kentucky 40506
| | - Michael W W Adams
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602
| | - Paul W King
- National Renewable Energy Laboratory, Golden, Colorado 80401
| | - Anne-Frances Miller
- From the Department of Chemistry, University of Kentucky, Lexington, Kentucky 40506.
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