201
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Kenney GE, Dassama LMK, Pandelia ME, Gizzi AS, Martinie RJ, Gao P, DeHart CJ, Schachner LF, Skinner OS, Ro SY, Zhu X, Sadek M, Thomas PM, Almo SC, Bollinger JM, Krebs C, Kelleher NL, Rosenzweig AC. The biosynthesis of methanobactin. Science 2018; 359:1411-1416. [PMID: 29567715 DOI: 10.1126/science.aap9437] [Citation(s) in RCA: 91] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Accepted: 02/07/2018] [Indexed: 11/02/2022]
Abstract
Metal homeostasis poses a major challenge to microbes, which must acquire scarce elements for core metabolic processes. Methanobactin, an extensively modified copper-chelating peptide, was one of the earliest natural products shown to enable microbial acquisition of a metal other than iron. We describe the core biosynthetic machinery responsible for the characteristic posttranslational modifications that grant methanobactin its specificity and affinity for copper. A heterodimer comprising MbnB, a DUF692 family iron enzyme, and MbnC, a protein from a previously unknown family, performs a dioxygen-dependent four-electron oxidation of the precursor peptide (MbnA) to install an oxazolone and an adjacent thioamide, the characteristic methanobactin bidentate copper ligands. MbnB and MbnC homologs are encoded together and separately in many bacterial genomes, suggesting functions beyond their roles in methanobactin biosynthesis.
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Affiliation(s)
- Grace E Kenney
- Department of Molecular Biosciences and Department of Chemistry, Northwestern University, Evanston, IL 60208, USA
| | - Laura M K Dassama
- Department of Molecular Biosciences and Department of Chemistry, Northwestern University, Evanston, IL 60208, USA
| | | | - Anthony S Gizzi
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Ryan J Martinie
- Department of Chemistry and Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Peng Gao
- Department of Molecular Biosciences and Department of Chemistry, Northwestern University, Evanston, IL 60208, USA
| | - Caroline J DeHart
- Department of Molecular Biosciences and Department of Chemistry, Northwestern University, Evanston, IL 60208, USA
| | - Luis F Schachner
- Department of Molecular Biosciences and Department of Chemistry, Northwestern University, Evanston, IL 60208, USA
| | - Owen S Skinner
- Department of Molecular Biosciences and Department of Chemistry, Northwestern University, Evanston, IL 60208, USA
| | - Soo Y Ro
- Department of Molecular Biosciences and Department of Chemistry, Northwestern University, Evanston, IL 60208, USA
| | - Xiao Zhu
- Department of Molecular Biosciences and Department of Chemistry, Northwestern University, Evanston, IL 60208, USA
| | - Monica Sadek
- Department of Molecular Biosciences and Department of Chemistry, Northwestern University, Evanston, IL 60208, USA
| | - Paul M Thomas
- Department of Molecular Biosciences and Department of Chemistry, Northwestern University, Evanston, IL 60208, USA
| | - Steven C Almo
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - J Martin Bollinger
- Department of Chemistry and Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Carsten Krebs
- Department of Chemistry and Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Neil L Kelleher
- Department of Molecular Biosciences and Department of Chemistry, Northwestern University, Evanston, IL 60208, USA
| | - Amy C Rosenzweig
- Department of Molecular Biosciences and Department of Chemistry, Northwestern University, Evanston, IL 60208, USA.
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202
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Avilan L, Roumezi B, Risoul V, Bernard CS, Kpebe A, Belhadjhassine M, Rousset M, Brugna M, Latifi A. Phototrophic hydrogen production from a clostridial [FeFe] hydrogenase expressed in the heterocysts of the cyanobacterium Nostoc PCC 7120. Appl Microbiol Biotechnol 2018; 102:5775-5783. [DOI: 10.1007/s00253-018-8989-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Revised: 03/11/2018] [Accepted: 04/05/2018] [Indexed: 12/28/2022]
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203
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Electron Transfer to Nitrogenase in Different Genomic and Metabolic Backgrounds. J Bacteriol 2018; 200:JB.00757-17. [PMID: 29483165 DOI: 10.1128/jb.00757-17] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 02/16/2018] [Indexed: 11/20/2022] Open
Abstract
Nitrogenase catalyzes the reduction of dinitrogen (N2) using low-potential electrons from ferredoxin (Fd) or flavodoxin (Fld) through an ATP-dependent process. Since its emergence in an anaerobic chemoautotroph, this oxygen (O2)-sensitive enzyme complex has evolved to operate in a variety of genomic and metabolic backgrounds, including those of aerobes, anaerobes, chemotrophs, and phototrophs. However, whether pathways of electron delivery to nitrogenase are influenced by these different metabolic backgrounds is not well understood. Here, we report the distribution of homologs of Fds, Flds, and Fd-/Fld-reducing enzymes in 359 genomes of putative N2 fixers (diazotrophs). Six distinct lineages of nitrogenase were identified, and their distributions largely corresponded to differences in the host cells' ability to integrate O2 or light into energy metabolism. The predicted pathways of electron transfer to nitrogenase in aerobes, facultative anaerobes, and phototrophs varied from those in anaerobes at the levels of Fds/Flds used to reduce nitrogenase, the enzymes that generate reduced Fds/Flds, and the putative substrates of these enzymes. Proteins that putatively reduce Fd with hydrogen or pyruvate were enriched in anaerobes, while those that reduce Fd with NADH/NADPH were enriched in aerobes, facultative anaerobes, and anoxygenic phototrophs. The energy metabolism of aerobic, facultatively anaerobic, and anoxygenic phototrophic diazotrophs often yields reduced NADH/NADPH that is not sufficiently reduced to drive N2 reduction. At least two mechanisms have been acquired by these taxa to overcome this limitation and to generate electrons with potentials capable of reducing Fd. These include the bifurcation of electrons or the coupling of Fd reduction to reverse ion translocation.IMPORTANCE Nitrogen fixation supplies fixed nitrogen to cells from a variety of genomic and metabolic backgrounds, including those of aerobes, facultative anaerobes, chemotrophs, and phototrophs. Here, using informatics approaches applied to genomic data, we show that pathways of electron transfer to nitrogenase in metabolically diverse diazotrophic taxa have diversified primarily in response to host cells' acquired ability to integrate O2 or light into their energy metabolism. The acquisition of two key enzyme complexes enabled aerobic and facultatively anaerobic phototrophic taxa to generate electrons of sufficiently low potential to reduce nitrogenase: the bifurcation of electrons via the Fix complex or the coupling of Fd reduction to reverse ion translocation via the Rhodobacter nitrogen fixation (Rnf) complex.
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204
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Caserta G, Papini C, Adamska-Venkatesh A, Pecqueur L, Sommer C, Reijerse E, Lubitz W, Gauquelin C, Meynial-Salles I, Pramanik D, Artero V, Atta M, Del Barrio M, Faivre B, Fourmond V, Léger C, Fontecave M. Engineering an [FeFe]-Hydrogenase: Do Accessory Clusters Influence O 2 Resistance and Catalytic Bias? J Am Chem Soc 2018; 140:5516-5526. [PMID: 29595965 DOI: 10.1021/jacs.8b01689] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
[FeFe]-hydrogenases, HydAs, are unique biocatalysts for proton reduction to H2. However, they suffer from a number of drawbacks for biotechnological applications: size, number and diversity of metal cofactors, oxygen sensitivity. Here we show that HydA from Megasphaera elsdenii (MeHydA) displays significant resistance to O2. Furthermore, we produced a shorter version of this enzyme (MeH-HydA), lacking the N-terminal domain harboring the accessory FeS clusters. As shown by detailed spectroscopic and biochemical characterization, MeH-HydA displays the following interesting properties. First, a functional active site can be assembled in MeH-HydA in vitro, providing the enzyme with excellent hydrogenase activity. Second, the resistance of MeHydA to O2 is conserved in MeH-HydA. Third, MeH-HydA is more biased toward proton reduction than MeHydA, as the result of the truncation changing the rate limiting steps in catalysis. This work shows that it is possible to engineer HydA to generate an active hydrogenase that combines the resistance of the most resistant HydAs and the simplicity of algal HydAs, containing only the H-cluster.
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Affiliation(s)
- Giorgio Caserta
- Laboratoire de Chimie des Processus Biologiques , Collège de France, Université Pierre et Marie Curie, CNRS UMR 8229, PSL Research University , 11 place Marcelin Berthelot , 75005 Paris , France
| | - Cecilia Papini
- Laboratoire de Chimie des Processus Biologiques , Collège de France, Université Pierre et Marie Curie, CNRS UMR 8229, PSL Research University , 11 place Marcelin Berthelot , 75005 Paris , France
| | - Agnieszka Adamska-Venkatesh
- Max-Planck-Institut für Chemische Energiekonversion , Stiftstrasse 34-36 , 45470 Mülheim an der Ruhr , Germany
| | - Ludovic Pecqueur
- Laboratoire de Chimie des Processus Biologiques , Collège de France, Université Pierre et Marie Curie, CNRS UMR 8229, PSL Research University , 11 place Marcelin Berthelot , 75005 Paris , France
| | - Constanze Sommer
- Max-Planck-Institut für Chemische Energiekonversion , Stiftstrasse 34-36 , 45470 Mülheim an der Ruhr , Germany
| | - Edward Reijerse
- Max-Planck-Institut für Chemische Energiekonversion , Stiftstrasse 34-36 , 45470 Mülheim an der Ruhr , Germany
| | - Wolfgang Lubitz
- Max-Planck-Institut für Chemische Energiekonversion , Stiftstrasse 34-36 , 45470 Mülheim an der Ruhr , Germany
| | - Charles Gauquelin
- LISBP , Université de Toulouse, CNRS, INRA, INSA , Toulouse , France
| | | | - Debajyoti Pramanik
- Laboratoire de Chimie et Biologie des Métaux , Université Grenoble Alpes, CEA/BIG, CNRS , 17 rue des martyrs , 38000 Grenoble , France
| | - Vincent Artero
- Laboratoire de Chimie et Biologie des Métaux , Université Grenoble Alpes, CEA/BIG, CNRS , 17 rue des martyrs , 38000 Grenoble , France
| | - Mohamed Atta
- Laboratoire de Chimie et Biologie des Métaux , Université Grenoble Alpes, CEA/BIG, CNRS , 17 rue des martyrs , 38000 Grenoble , France
| | - Melisa Del Barrio
- Aix Marseille Université , CNRS, Laboratoire de Bioénergétique et Ingénierie des Protéines UMR 7281 , 13400 Marseille , France
| | - Bruno Faivre
- Laboratoire de Chimie des Processus Biologiques , Collège de France, Université Pierre et Marie Curie, CNRS UMR 8229, PSL Research University , 11 place Marcelin Berthelot , 75005 Paris , France
| | - Vincent Fourmond
- Aix Marseille Université , CNRS, Laboratoire de Bioénergétique et Ingénierie des Protéines UMR 7281 , 13400 Marseille , France
| | - Christophe Léger
- Aix Marseille Université , CNRS, Laboratoire de Bioénergétique et Ingénierie des Protéines UMR 7281 , 13400 Marseille , France
| | - Marc Fontecave
- Laboratoire de Chimie des Processus Biologiques , Collège de France, Université Pierre et Marie Curie, CNRS UMR 8229, PSL Research University , 11 place Marcelin Berthelot , 75005 Paris , France
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205
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Gutekunst K, Hoffmann D, Westernströer U, Schulz R, Garbe-Schönberg D, Appel J. In-vivo turnover frequency of the cyanobacterial NiFe-hydrogenase during photohydrogen production outperforms in-vitro systems. Sci Rep 2018; 8:6083. [PMID: 29666458 PMCID: PMC5904137 DOI: 10.1038/s41598-018-24430-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 03/28/2018] [Indexed: 12/12/2022] Open
Abstract
Cyanobacteria provide all components for sunlight driven biohydrogen production. Their bidirectional NiFe-hydrogenase is resistant against low levels of oxygen with a preference for hydrogen evolution. However, until now it was unclear if its catalytic efficiency can keep pace with the photosynthetic electron transfer rate. We identified NikKLMQO (sll0381-sll0385) as a nickel transporter, which is required for hydrogen production. ICP-MS measurements were used to quantify hydrogenase molecules per cell. We found 400 to 2000 hydrogenase molecules per cell depending on the conditions. In-vivo turnover frequencies of the enzyme ranged from 62 H2/s in the wild type to 120 H2/s in a mutant during photohydrogen production. These frequencies are above maximum in-vivo photosynthetic electron transfer rates of 47 e-/s (equivalent to 24 H2/s). They are also above those of existing in-vitro systems working with unlimited electron supply and show that in-vivo photohydrogen production is limited by electron delivery to the enzyme.
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Affiliation(s)
- Kirstin Gutekunst
- Botanical Institute, Christian-Albrechts-University, 24118, Kiel, Germany
| | - Dörte Hoffmann
- Botanical Institute, Christian-Albrechts-University, 24118, Kiel, Germany
| | | | - Rüdiger Schulz
- Botanical Institute, Christian-Albrechts-University, 24118, Kiel, Germany
| | | | - Jens Appel
- Botanical Institute, Christian-Albrechts-University, 24118, Kiel, Germany.
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206
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A [4Fe-4S]-Fe(CO)(CN)-L-cysteine intermediate is the first organometallic precursor in [FeFe] hydrogenase H-cluster bioassembly. Nat Chem 2018; 10:555-560. [PMID: 29632334 PMCID: PMC6380689 DOI: 10.1038/s41557-018-0026-7] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Accepted: 02/14/2018] [Indexed: 12/27/2022]
Abstract
Biosynthesis of the [FeFe] hydrogenase active site (the 'H-cluster') requires the interplay of multiple proteins and small molecules. Among them, the radical S-adenosylmethionine enzyme HydG, a tyrosine lyase, has been proposed to generate a complex that contains an Fe(CO)2(CN) moiety that is eventually incorporated into the H-cluster. Here we describe the characterization of an intermediate in the HydG reaction: a [4Fe-4S][(Cys)Fe(CO)(CN)] species, 'Complex A', in which a CO, a CN- and a cysteine (Cys) molecule bind to the unique 'dangler' Fe site of the auxiliary [5Fe-4S] cluster of HydG. The identification of this intermediate-the first organometallic precursor to the H-cluster-validates the previously hypothesized HydG reaction cycle and provides a basis for elucidating the biosynthetic origin of other moieties of the H-cluster.
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207
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Kwon S, Nishitani Y, Hirao Y, Kanai T, Atomi H, Miki K. Structure of a [NiFe] hydrogenase maturation protease HycI provides insights into its substrate selectivity. Biochem Biophys Res Commun 2018. [DOI: 10.1016/j.bbrc.2018.03.058] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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208
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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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209
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Roles of the F-domain in [FeFe] hydrogenase. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2018; 1859:69-77. [DOI: 10.1016/j.bbabio.2017.08.010] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Revised: 08/16/2017] [Accepted: 08/19/2017] [Indexed: 12/31/2022]
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210
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Abby SS, Melcher M, Kerou M, Krupovic M, Stieglmeier M, Rossel C, Pfeifer K, Schleper C. Candidatus Nitrosocaldus cavascurensis, an Ammonia Oxidizing, Extremely Thermophilic Archaeon with a Highly Mobile Genome. Front Microbiol 2018; 9:28. [PMID: 29434576 PMCID: PMC5797428 DOI: 10.3389/fmicb.2018.00028] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Accepted: 01/08/2018] [Indexed: 12/22/2022] Open
Abstract
Ammonia oxidizing archaea (AOA) of the phylum Thaumarchaeota are widespread in moderate environments but their occurrence and activity has also been demonstrated in hot springs. Here we present the first enrichment of a thermophilic representative with a sequenced genome, which facilitates the search for adaptive strategies and for traits that shape the evolution of Thaumarchaeota. Candidatus Nitrosocaldus cavascurensis has been enriched from a hot spring in Ischia, Italy. It grows optimally at 68°C under chemolithoautotrophic conditions on ammonia or urea converting ammonia stoichiometrically into nitrite with a generation time of approximately 23 h. Phylogenetic analyses based on ribosomal proteins place the organism as a sister group to all known mesophilic AOA. The 1.58 Mb genome of Ca. N. cavascurensis harbors an amoAXCB gene cluster encoding ammonia monooxygenase and genes for a 3-hydroxypropionate/4-hydroxybutyrate pathway for autotrophic carbon fixation, but also genes that indicate potential alternative energy metabolisms. Although a bona fide gene for nitrite reductase is missing, the organism is sensitive to NO-scavenging, underlining the potential importance of this compound for AOA metabolism. Ca. N. cavascurensis is distinct from all other AOA in its gene repertoire for replication, cell division and repair. Its genome has an impressive array of mobile genetic elements and other recently acquired gene sets, including conjugative systems, a provirus, transposons and cell appendages. Some of these elements indicate recent exchange with the environment, whereas others seem to have been domesticated and might convey crucial metabolic traits.
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Affiliation(s)
- Sophie S Abby
- Division of Archaea Biology and Ecogenomics, Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria.,Laboratoire Techniques de l'Ingénierie Médicale et de la Complexité - Informatique, Mathématiques et Applications, Centre National de la Recherche Scientifique, Université Grenoble Alpes, Grenoble, France
| | - Michael Melcher
- Division of Archaea Biology and Ecogenomics, Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria
| | - Melina Kerou
- Division of Archaea Biology and Ecogenomics, Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria
| | - Mart Krupovic
- Unité Biologie Moléculaire du Gène chez les Extrêmophiles, Institut Pasteur, Paris, France
| | - Michaela Stieglmeier
- Division of Archaea Biology and Ecogenomics, Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria
| | - Claudia Rossel
- Division of Archaea Biology and Ecogenomics, Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria
| | - Kevin Pfeifer
- Division of Archaea Biology and Ecogenomics, Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria
| | - Christa Schleper
- Division of Archaea Biology and Ecogenomics, Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria
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211
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Freibert SA, Weiler BD, Bill E, Pierik AJ, Mühlenhoff U, Lill R. Biochemical Reconstitution and Spectroscopic Analysis of Iron-Sulfur Proteins. Methods Enzymol 2018; 599:197-226. [PMID: 29746240 DOI: 10.1016/bs.mie.2017.11.034] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
Iron-sulfur (Fe/S) proteins are involved in numerous key biological functions such as respiration, metabolic processes, protein translation, DNA synthesis, and DNA repair. The simplest types of Fe/S clusters include [2Fe-2S], [3Fe-4S], and [4Fe-4S] forms that sometimes are present in multiple copies. De novo assembly of Fe/S cofactors and their insertion into apoproteins in living cells requires complex proteinaceous machineries that are frequently highly conserved. In eukaryotes such as yeast and mammals, the mitochondrial iron-sulfur cluster assembly machinery and the cytosolic iron-sulfur protein assembly system consist of more than 30 components that cooperate in the generation of some 50 cellular Fe/S proteins. Both the mechanistic dissection of the intracellular Fe/S protein assembly pathways and the identification and characterization of Fe/S proteins rely on tool boxes of in vitro and in vivo methods. These cell biological, biochemical, and biophysical techniques help to determine the extent, stability, and type of bound Fe/S cluster. They also serve to distinguish bona fide Fe/S proteins from other metal-binding proteins containing similar cofactor coordination motifs. Here, we present a collection of in vitro methods that have proven useful for basic biochemical and biophysical characterization of Fe/S proteins. First, we describe the chemical assembly of [2Fe-2S] or [4Fe-4S] clusters on purified apoproteins. Then, we summarize a reconstitution system reproducing the de novo synthesis of a [2Fe-2S] cluster in mitochondria. Finally, we explain the use of UV-vis, CD, electron paramagnetic resonance, and Mössbauer spectroscopy for the routine characterization of Fe/S proteins.
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Affiliation(s)
| | | | - Eckhard Bill
- Max-Planck-Institut für Chemische Energiekonversion, Mülheim an der Ruhr, Germany
| | - Antonio J Pierik
- Chemistry and Biochemistry, Technical University of Kaiserlautern, Kaiserlautern, Germany
| | | | - Roland Lill
- Institut für Zytobiologie, Philipps-Universität, Marburg, Germany; LOEWE Zentrum für Synthetische Mikrobiologie SynMikro, Marburg, Germany.
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212
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Zaffaroni R, Detz RJ, van der Vlugt JI, Reek JNH. A Functional Hydrogenase Mimic Chemisorbed onto Fluorine-Doped Tin Oxide Electrodes: A Strategy towards Water Splitting Devices. CHEMSUSCHEM 2018; 11:209-218. [PMID: 29077275 PMCID: PMC5814736 DOI: 10.1002/cssc.201701757] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Revised: 10/26/2017] [Indexed: 06/07/2023]
Abstract
A diiron benzenedithiolate hydrogen-evolving catalyst immobilized onto fluorine-doped tin oxide (FTO) electrodes is prepared, characterized, and studied in the context of the development of water splitting devices based on molecular components. FTO was chosen as the preferred electrode material owing to its conductive properties and electrochemical stability. An FTO nanocrystalline layer is also used to greatly improve the surface area of commercially available FTO while preserving the properties of the material. Electrodes bearing a covalently anchored diiron catalyst are shown to be competent for electrocatalytic hydrogen evolution from acidic aqueous media at relatively low overpotential (500 mV) with a faradaic efficiency close to unity. Compared with bulk solution catalysts, the catalyst immobilized onto the electrode surface operates at roughly 160 mV lower overpotentials, yet with similar rates.
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Affiliation(s)
- Riccardo Zaffaroni
- Van't Hoff Institute for Molecular SciencesUniversity of AmsterdamScience Park 9041098XHAmsterdamThe Netherlands
| | - Remko J. Detz
- Van't Hoff Institute for Molecular SciencesUniversity of AmsterdamScience Park 9041098XHAmsterdamThe Netherlands
| | - Jarl Ivar van der Vlugt
- Van't Hoff Institute for Molecular SciencesUniversity of AmsterdamScience Park 9041098XHAmsterdamThe Netherlands
| | - Joost N. H. Reek
- Van't Hoff Institute for Molecular SciencesUniversity of AmsterdamScience Park 9041098XHAmsterdamThe Netherlands
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213
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Chongdar N, Birrell JA, Pawlak K, Sommer C, Reijerse EJ, Rüdiger O, Lubitz W, Ogata H. Unique Spectroscopic Properties of the H-Cluster in a Putative Sensory [FeFe] Hydrogenase. J Am Chem Soc 2018; 140:1057-1068. [PMID: 29251926 DOI: 10.1021/jacs.7b11287] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Sensory type [FeFe] hydrogenases are predicted to play a role in transcriptional regulation by detecting the H2 level of the cellular environment. These hydrogenases contain the hydrogenase domain with distinct modifications in the active site pocket, followed by a Per-Arnt-Sim (PAS) domain. As yet, neither the physiological function nor the biochemical or spectroscopic properties of these enzymes have been explored. Here, we present the characterization of an artificially maturated, putative sensory [FeFe] hydrogenase from Thermotoga maritima (HydS). This enzyme shows lower hydrogen conversion activity than prototypical [FeFe] hydrogenases and a reduced inhibition by CO. Using FTIR spectroelectrochemistry and EPR spectroscopy, three redox states of the active site were identified. The spectroscopic signatures of the most oxidized state closely resemble those of the Hox state from the prototypical [FeFe] hydrogenases, while the FTIR spectra of both singly and doubly reduced states show large differences. The FTIR bands of both the reduced states are strongly red-shifted relative to the Hox state, indicating reduction at the diiron site, but with retention of the bridging CO ligand. The unique functional and spectroscopic features of HydS are discussed with regard to the possible role of altered amino acid residues influencing the electronic properties of the H-cluster.
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Affiliation(s)
- Nipa Chongdar
- Max Planck Institute for Chemical Energy Conversion , Stiftstrasse 34-36, D45470 Mülheim an der Ruhr, Germany
| | - James A Birrell
- Max Planck Institute for Chemical Energy Conversion , Stiftstrasse 34-36, D45470 Mülheim an der Ruhr, Germany
| | - Krzysztof Pawlak
- Max Planck Institute for Chemical Energy Conversion , Stiftstrasse 34-36, D45470 Mülheim an der Ruhr, Germany
| | - Constanze Sommer
- Max Planck Institute for Chemical Energy Conversion , Stiftstrasse 34-36, D45470 Mülheim an der Ruhr, Germany
| | - Edward J Reijerse
- Max Planck Institute for Chemical Energy Conversion , Stiftstrasse 34-36, D45470 Mülheim an der Ruhr, Germany
| | - Olaf Rüdiger
- Max Planck Institute for Chemical Energy Conversion , Stiftstrasse 34-36, D45470 Mülheim an der Ruhr, Germany
| | - Wolfgang Lubitz
- Max Planck Institute for Chemical Energy Conversion , Stiftstrasse 34-36, D45470 Mülheim an der Ruhr, Germany
| | - Hideaki Ogata
- Max Planck Institute for Chemical Energy Conversion , Stiftstrasse 34-36, D45470 Mülheim an der Ruhr, Germany.,Institute of Low Temperature Science, Hokkaido University , Kita19 Nishi8, Kita-ku, 060-0819 Sapporo, Japan
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Dipasquale L, Pradhan N, d’Ippolito G, Fontana A. Potential of Hydrogen Fermentative Pathways in Marine Thermophilic Bacteria: Dark Fermentation and Capnophilic Lactic Fermentation in Thermotoga and Pseudothermotoga Species. GRAND CHALLENGES IN MARINE BIOTECHNOLOGY 2018. [DOI: 10.1007/978-3-319-69075-9_6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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216
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Kertess L, Adamska-Venkatesh A, Rodríguez-Maciá P, Rüdiger O, Lubitz W, Happe T. Influence of the [4Fe-4S] cluster coordinating cysteines on active site maturation and catalytic properties of C. reinhardtii [FeFe]-hydrogenase. Chem Sci 2017; 8:8127-8137. [PMID: 29568461 PMCID: PMC5855289 DOI: 10.1039/c7sc03444j] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Accepted: 10/05/2017] [Indexed: 11/24/2022] Open
Abstract
Alteration of the [4Fe–4S] cluster coordinating cysteines reveals their individual importance for [4Fe–4S] cluster binding, [2Fe] insertion and catalytic turnover.
[FeFe]-Hydrogenases catalyze the evolution and oxidation of hydrogen using a characteristic cofactor, termed the H-cluster. This comprises an all cysteine coordinated [4Fe–4S] cluster and a unique [2Fe] moiety, coupled together via a single cysteine. The coordination of the [4Fe–4S] cluster in HydA1 from Chlamydomonas reinhardtii was altered by single exchange of each cysteine (C115, C170, C362, and C366) with alanine, aspartate, or serine using site-directed mutagenesis. In contrast to cysteine 115, the other three cysteines were found to be dispensable for stable [4Fe–4S] cluster incorporation based on iron determination, UV/vis spectroscopy and electron paramagnetic resonance. However, the presence of a preformed [4Fe–4S] cluster alone does not guarantee stable incorporation of the [2Fe] cluster. Only variants C170D, C170S, C362D, and C362S showed characteristic signals for an inserted [2Fe] cluster in Fourier-transform infrared spectroscopy. Hydrogen evolution and oxidation were observed for these variants in solution based assays and protein-film electrochemistry. Catalytic activity was lowered for all variants and the ability to operate in either direction was also influenced.
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Affiliation(s)
- Leonie Kertess
- AG Photobiotechnologie , Lehrstuhl für Biochemie der Pflanzen , Ruhr Universität Bochum , Universitätsstr. 150 , 44801 Bochum , Germany .
| | - Agnieszka Adamska-Venkatesh
- Max Planck Institute for Chemical Energy Conversion , Stiftstrasse 34-36 , 45470 Mülheim an der Ruhr , Germany
| | - Patricia Rodríguez-Maciá
- Max Planck Institute for Chemical Energy Conversion , Stiftstrasse 34-36 , 45470 Mülheim an der Ruhr , Germany
| | - Olaf Rüdiger
- Max Planck Institute for Chemical Energy Conversion , Stiftstrasse 34-36 , 45470 Mülheim an der Ruhr , Germany
| | - Wolfgang Lubitz
- Max Planck Institute for Chemical Energy Conversion , Stiftstrasse 34-36 , 45470 Mülheim an der Ruhr , Germany
| | - Thomas Happe
- AG Photobiotechnologie , Lehrstuhl für Biochemie der Pflanzen , Ruhr Universität Bochum , Universitätsstr. 150 , 44801 Bochum , Germany .
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217
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Pelmenschikov V, Birrell JA, Pham CC, Mishra N, Wang H, Sommer C, Reijerse E, Richers CP, Tamasaku K, Yoda Y, Rauchfuss TB, Lubitz W, Cramer SP. Reaction Coordinate Leading to H 2 Production in [FeFe]-Hydrogenase Identified by Nuclear Resonance Vibrational Spectroscopy and Density Functional Theory. J Am Chem Soc 2017; 139:16894-16902. [PMID: 29054130 PMCID: PMC5699932 DOI: 10.1021/jacs.7b09751] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
[FeFe]-hydrogenases are metalloenzymes that reversibly reduce protons to molecular hydrogen at exceptionally high rates. We have characterized the catalytically competent hydride state (Hhyd) in the [FeFe]-hydrogenases from both Chlamydomonas reinhardtii and Desulfovibrio desulfuricans using 57Fe nuclear resonance vibrational spectroscopy (NRVS) and density functional theory (DFT). H/D exchange identified two Fe-H bending modes originating from the binuclear iron cofactor. DFT calculations show that these spectral features result from an iron-bound terminal hydride, and the Fe-H vibrational frequencies being highly dependent on interactions between the amine base of the catalytic cofactor with both hydride and the conserved cysteine terminating the proton transfer chain to the active site. The results indicate that Hhyd is the catalytic state one step prior to H2 formation. The observed vibrational spectrum, therefore, provides mechanistic insight into the reaction coordinate for H2 bond formation by [FeFe]-hydrogenases.
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Affiliation(s)
- Vladimir Pelmenschikov
- Institut für Chemie, Technische Universität Berlin , Strasse des 17 Juni 135, 10623 Berlin, Germany
| | - James A Birrell
- Max-Planck-Institut für Chemische Energiekonversion , Stiftstrasse 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Cindy C Pham
- Department of Chemistry, University of California, Davis , One Shields Avenue, Davis, California 95616, United States
| | - Nakul Mishra
- Department of Chemistry, University of California, Davis , One Shields Avenue, Davis, California 95616, United States
| | - Hongxin Wang
- Department of Chemistry, University of California, Davis , One Shields Avenue, Davis, California 95616, United States
| | - Constanze Sommer
- Max-Planck-Institut für Chemische Energiekonversion , Stiftstrasse 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Edward Reijerse
- Max-Planck-Institut für Chemische Energiekonversion , Stiftstrasse 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Casseday P Richers
- School of Chemical Sciences, University of Illinois , 600 S. Mathews Avenue, Urbana, Illinois 61801, United States
| | - Kenji Tamasaku
- JASRI , Spring-8, 1-1-1 Kouto, Mikazuki-cho, Sayo-gun, Hyogo 679-5198, Japan
| | - Yoshitaka Yoda
- JASRI , Spring-8, 1-1-1 Kouto, Mikazuki-cho, Sayo-gun, Hyogo 679-5198, Japan
| | - Thomas B Rauchfuss
- School of Chemical Sciences, University of Illinois , 600 S. Mathews Avenue, Urbana, Illinois 61801, United States
| | - Wolfgang Lubitz
- Max-Planck-Institut für Chemische Energiekonversion , Stiftstrasse 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Stephen P Cramer
- Department of Chemistry, University of California, Davis , One Shields Avenue, Davis, California 95616, United States
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218
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Greene BL, Vansuch GE, Chica BC, Adams MWW, Dyer RB. Applications of Photogating and Time Resolved Spectroscopy to Mechanistic Studies of Hydrogenases. Acc Chem Res 2017; 50:2718-2726. [PMID: 29083854 DOI: 10.1021/acs.accounts.7b00356] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Rapid and facile redox chemistry is exemplified in nature by the oxidoreductases, the class of enzymes that catalyze electron transfer (ET) from a donor to an acceptor. The key role of oxidoreductases in metabolism and biosynthesis has imposed evolutionary pressure to enhance enzyme efficiency, pushing some toward the diffusion limit. Understanding the detailed molecular mechanisms of these highly optimized enzymes would provide an important foundation for the rational design of catalysts for multielectron chemistry, including fuel production. The hydrogenases (H2ases) are the oxidoreductases that catalyze the most basic electron and proton transfer reactions relevant to fuel production, the interconversion of protons and hydrogen, with kcat > 103 s-1. Thus, they provide a model system for studying the efficiency exhibited by oxidoreductases. Because of the extraordinarily fast catalytic rates of these enzymes, their mechanisms have been difficult to study directly but instead have been inferred from structural and steady-state measurements. Although informative, the kinetic competency of observed equilibrium steps can only be suggested by these methods, not demonstrated, because the fundamental (fast) catalytic steps remain unresolved, resulting in minimal insight regarding the underlying ET and proton transfer (PT) events. Motivated by this gap in understanding, we developed an approach capable of observing elementary ET and PT during such fast enzyme turnover by combining a laser-induced potential jump with time-resolved spectroscopy. The potential jump initiates enzyme turnover by utilizing a short-pulsed laser to release a "caged" electron from a nanomaterial or NAD(P)H, which is then captured by a mediator such as methyl viologen. The subsequent enzyme reduction and turnover are monitored by transient absorption spectroscopy in the visible or mid-IR spectral regions. The method is completely general and in principle can be applied to any catalytic redox reaction. In the case of hydrogenases, time-resolved infrared spectroscopy of the active site CO ligands is particularly informative since the IR frequencies are exquisitely sensitive to the redox and protonation states. Using this methodology, we have developed a description of the catalytic mechanism of the Pyrococcus furiosus [NiFe]-hydrogenase by demonstrating the kinetic and chemical competency of equilibrium states and by invoking new intermediates. Additionally, the pre-steady-state kinetics revealed a distinct role of proton tunneling in concerted electron-proton transfer (EPT) modulated by a conserved glutamic acid residue. Similar multisite EPT processes have been implicated in numerous enzymes but have not been demonstrated explicitly. These methods have also been successfully applied to an electron bifurcating [FeFe]-H2ase from Thermotoga maritima, establishing the kinetic competency of the Hox, Hred, and Hsred intermediates of the [FeFe] enzyme. These results provide fundamental insight on the factors that control low barrier proton and electron flow in enzymes and thus provide a foundation for the rational design of reversible biomimetic catalysts.
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Affiliation(s)
- Brandon L. Greene
- Department
of Chemistry, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, United States
| | - Gregory E. Vansuch
- Department
of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, Georgia 30322, United States
| | - Bryant C. Chica
- Department
of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, Georgia 30322, United States
| | - Michael W. W. Adams
- Department
of Biochemistry and Molecular Biology, University of Georgia, B122 Life
Sciences Bldg., Athens, Georgia 30602, United States
| | - R. Brian Dyer
- Department
of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, Georgia 30322, United States
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219
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Maio N, Rouault TA. Mammalian Fe-S proteins: definition of a consensus motif recognized by the co-chaperone HSC20. Metallomics 2017; 8:1032-1046. [PMID: 27714045 DOI: 10.1039/c6mt00167j] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Iron-sulfur (Fe-S) clusters are inorganic cofactors that are fundamental to several biological processes in all three kingdoms of life. In most organisms, Fe-S clusters are initially assembled on a scaffold protein, ISCU, and subsequently transferred to target proteins or to intermediate carriers by a dedicated chaperone/co-chaperone system. The delivery of assembled Fe-S clusters to recipient proteins is a crucial step in the biogenesis of Fe-S proteins, and, in mammals, it relies on the activity of a multiprotein transfer complex that contains the chaperone HSPA9, the co-chaperone HSC20 and the scaffold ISCU. How the transfer complex efficiently engages recipient Fe-S target proteins involves specific protein interactions that are not fully understood. This mini review focuses on recent insights into the molecular mechanism of amino acid motif recognition and discrimination by the co-chaperone HSC20, which guides Fe-S cluster delivery.
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Affiliation(s)
- N Maio
- Molecular Medicine Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, 9000 Rockville Pike, 20892 Bethesda, MD, USA.
| | - T A Rouault
- Molecular Medicine Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, 9000 Rockville Pike, 20892 Bethesda, MD, USA.
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220
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Burkhardt L, Holzwarth M, Plietker B, Bauer M. Detection and Characterization of Hydride Ligands in Iron Complexes by High-Resolution Hard X-ray Spectroscopy and Implications for Catalytic Processes. Inorg Chem 2017; 56:13300-13310. [PMID: 29058447 DOI: 10.1021/acs.inorgchem.7b02063] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Two hydride catalysts [Fe(CO)(dppp)H(NO)] (dppp = 1,3-bis(diphenylphosphino)propane) and [Fe(CO)H(NO)(PPh3)2] in comparison with nonhydride analogues [Fe(dppe)(NO)2] (dppe = 1,3-bis(diphenylphosphino)ethane) and [Fe(NO)2(PPh3)2] are investigated with a combination of valence-to-core X-ray emission spectroscopy (VtC-XES) and high-energy resolution fluorescence detected X-ray absorption near-edge structure (HERFD-XANES). To fully understand the experiments and to obtain precise information about molecular levels being involved in the spectral signals, time-dependent density functional theory (TD-DFT) calculations and ground state density functional theory (DFT) calculations are necessary. An excellent agreement between experiment and theory allows the identification of particular spectral signals of the Fe-H group. Antibonding Fe-H interactions clearly contribute to pre-edge signals in HERFD-XANES spectra, while bonding Fe-H interactions cause characteristic signatures in the VtC-XES spectra. The sensitivity of both methods with respect to the Fe-H distance is demonstrated by a scanning simulation approach. The results open the way to study metal hydride complexes in situ, their formation, and their fate during catalytic reactions, using high-resolution XANES and valence-to-core X-ray emission spectroscopy.
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Affiliation(s)
- Lukas Burkhardt
- Department Chemie, Universität Paderborn , Warburger Straße 100, D-33098 Paderborn, Germany
| | - Michael Holzwarth
- Institut für Organische Chemie, Universität Stuttgart , Pfaffenwaldring 55, D-70569 Stuttgart, Germany
| | - Bernd Plietker
- Institut für Organische Chemie, Universität Stuttgart , Pfaffenwaldring 55, D-70569 Stuttgart, Germany
| | - Matthias Bauer
- Department Chemie, Universität Paderborn , Warburger Straße 100, D-33098 Paderborn, Germany
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221
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Abstract
Numerous recent developments in the biochemistry, molecular biology, and physiology of formate and H2 metabolism and of the [NiFe]-hydrogenase (Hyd) cofactor biosynthetic machinery are highlighted. Formate export and import by the aquaporin-like pentameric formate channel FocA is governed by interaction with pyruvate formate-lyase, the enzyme that generates formate. Formate is disproportionated by the reversible formate hydrogenlyase (FHL) complex, which has been isolated, allowing biochemical dissection of evolutionary parallels with complex I of the respiratory chain. A recently identified sulfido-ligand attached to Mo in the active site of formate dehydrogenases led to the proposal of a modified catalytic mechanism. Structural analysis of the homologous, H2-oxidizing Hyd-1 and Hyd-5 identified a novel proximal [4Fe-3S] cluster in the small subunit involved in conferring oxygen tolerance to the enzymes. Synthesis of Salmonella Typhimurium Hyd-5 occurs aerobically, which is novel for an enterobacterial Hyd. The O2-sensitive Hyd-2 enzyme has been shown to be reversible: it presumably acts as a conformational proton pump in the H2-oxidizing mode and is capable of coupling reverse electron transport to drive H2 release. The structural characterization of all the Hyp maturation proteins has given new impulse to studies on the biosynthesis of the Fe(CN)2CO moiety of the [NiFe] cofactor. It is synthesized on a Hyp-scaffold complex, mainly comprising HypC and HypD, before insertion into the apo-large subunit. Finally, clear evidence now exists indicating that Escherichia coli can mature Hyd enzymes differentially, depending on metal ion availability and the prevailing metabolic state. Notably, Hyd-3 of the FHL complex takes precedence over the H2-oxidizing enzymes.
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222
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Kositzki R, Mebs S, Schuth N, Leidel N, Schwartz L, Karnahl M, Wittkamp F, Daunke D, Grohmann A, Apfel UP, Gloaguen F, Ott S, Haumann M. Electronic and molecular structure relations in diiron compounds mimicking the [FeFe]-hydrogenase active site studied by X-ray spectroscopy and quantum chemistry. Dalton Trans 2017; 46:12544-12557. [PMID: 28905949 DOI: 10.1039/c7dt02720f] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Synthetic diiron compounds of the general formula Fe2(μ-S2R)(CO)n(L)6-n (R = alkyl or aromatic groups; L = CN- or phosphines) are versatile models for the active-site cofactor of hydrogen turnover in [FeFe]-hydrogenases. A series of 18 diiron compounds, containing mostly a dithiolate bridge and terminal ligands of increasing complexity, was characterized by X-ray absorption and emission spectroscopy in combination with density functional theory. Fe K-edge absorption and Kβ main-line emission spectra revealed the varying geometry and the low-spin state of the Fe(i) centers. Good agreement between experimental and calculated core-to-valence-excitation absorption and radiative valence-to-core-decay emission spectra revealed correlations between spectroscopic and structural features and provided access to the electronic configuration. Four main effects on the diiron core were identified, which were preferentially related to variation either of the dithiolate or of the terminal ligands. Alteration of the dithiolate bridge affected mainly the Fe-Fe bond strength, while more potent donor substitution and ligand field asymmetrization changed the metal charge and valence level localization. In contrast, cyanide ligation altered all relevant properties and, in particular, the frontier molecular orbital energies of the diiron core. Mutual benchmarking of experimental and theoretical parameters provides guidelines to verify the electronic properties of related diiron compounds.
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Affiliation(s)
- Ramona Kositzki
- Freie Universität Berlin, Fachbereich Physik, 14195 Berlin, Germany.
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223
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A Review of Hydrogen Production by Photosynthetic Organisms Using Whole-Cell and Cell-Free Systems. Appl Biochem Biotechnol 2017; 183:503-519. [DOI: 10.1007/s12010-017-2576-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Accepted: 08/02/2017] [Indexed: 10/18/2022]
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224
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Danczak RE, Johnston MD, Kenah C, Slattery M, Wrighton KC, Wilkins MJ. Members of the Candidate Phyla Radiation are functionally differentiated by carbon- and nitrogen-cycling capabilities. MICROBIOME 2017; 5:112. [PMID: 28865481 PMCID: PMC5581439 DOI: 10.1186/s40168-017-0331-1] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Accepted: 08/23/2017] [Indexed: 05/20/2023]
Abstract
BACKGROUND The Candidate Phyla Radiation (CPR) is a recently described expansion of the tree of life that represents more than 15% of all bacterial diversity and potentially contains over 70 different phyla. Despite this broad phylogenetic variation, these microorganisms appear to feature little functional diversity, with members generally characterized as obligate fermenters. Additionally, much of the data describing CPR phyla has been generated from a limited number of environments, constraining our knowledge of their functional roles and biogeographical distribution. To expand our understanding of subsurface CPR microorganisms, we sampled four separate groundwater wells over 2 years across three Ohio counties. RESULTS Samples were analyzed using 16S rRNA gene amplicon and shotgun metagenomic sequencing. Amplicon results indicated that CPR members comprised between 2 and 20% of the microbial communities with relative abundances stable through time in Athens and Greene samples but dynamic in Licking groundwater. Shotgun metagenomic analyses generated 71 putative CPR genomes, representing roughly 32 known phyla and 2 putative new phyla, Candidatus Brownbacteria and Candidatus Hugbacteria. While these genomes largely mirrored metabolic characteristics of known CPR members, some features were previously uncharacterized. For instance, nitrite reductase, encoded by nirK, was found in four of our Parcubacteria genomes and multiple CPR genomes from other studies, indicating a potentially undescribed role for these microorganisms in denitrification. Additionally, glycoside hydrolase (GH) family profiles for our 71 genomes and over 2000 other CPR genomes were analyzed to characterize their carbon-processing potential. Although common trends were present throughout the radiation, differences highlighted potential mechanisms that could allow microorganisms across the CPR to occupy various subsurface niches. For example, members of the Microgenomates superphylum appear to potentially degrade a wider range of carbon substrates than other CPR phyla. CONCLUSIONS CPR members are present across a range of environments and often constitute a significant fraction of the microbial population in groundwater systems, particularly. Further sampling of such environments will resolve this portion of the tree of life at finer taxonomic levels, which is essential to solidify functional differences between members that populate this phylogenetically broad region of the tree of life.
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Affiliation(s)
- R E Danczak
- Department of Microbiology, The Ohio State University, Columbus, OH, USA
| | - M D Johnston
- School of Earth Sciences, The Ohio State University, Columbus, OH, USA
| | - C Kenah
- Ohio Environmental Protection Agency, Columbus, OH, USA
| | - M Slattery
- Ohio Environmental Protection Agency, Columbus, OH, USA
| | - K C Wrighton
- Department of Microbiology, The Ohio State University, Columbus, OH, USA
| | - M J Wilkins
- Department of Microbiology, The Ohio State University, Columbus, OH, USA.
- School of Earth Sciences, The Ohio State University, Columbus, OH, USA.
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225
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The structurally unique photosynthetic Chlorella variabilis NC64A hydrogenase does not interact with plant-type ferredoxins. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2017. [DOI: 10.1016/j.bbabio.2017.06.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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226
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Shepard EM, Byer AS, Broderick JB. Iron-Sulfur Cluster States of the Hydrogenase Maturase HydF. Biochemistry 2017; 56:4733-4734. [PMID: 28853860 DOI: 10.1021/acs.biochem.7b00735] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Eric M Shepard
- Department of Chemistry and Biochemistry, Montana State University , Bozeman, Montana 59717, United States
| | - Amanda S Byer
- Department of Chemistry and Biochemistry, Montana State University , Bozeman, Montana 59717, United States
| | - Joan B Broderick
- Department of Chemistry and Biochemistry, Montana State University , Bozeman, Montana 59717, United States
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227
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Artz JH, Zadvornyy OA, Mulder DW, King PW, Peters JW. Structural Characterization of Poised States in the Oxygen Sensitive Hydrogenases and Nitrogenases. Methods Enzymol 2017; 595:213-259. [PMID: 28882202 DOI: 10.1016/bs.mie.2017.07.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The crystallization of FeS cluster-containing proteins has been challenging due to their oxygen sensitivity, and yet these enzymes are involved in many critical catalytic reactions. The last few years have seen a wealth of innovative experiments designed to elucidate not just structural but mechanistic insights into FeS cluster enzymes. Here, we focus on the crystallization of hydrogenases, which catalyze the reversible reduction of protons to hydrogen, and nitrogenases, which reduce dinitrogen to ammonia. A specific focus is given to the different experimental parameters and strategies that are used to trap distinct enzyme states, specifically, oxidants, reductants, and gas treatments. Other themes presented here include the recent use of Cryo-EM, and how coupling various spectroscopies to crystallization is opening up new approaches for structural and mechanistic analysis.
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Affiliation(s)
- Jacob H Artz
- Institute of Biological Chemistry, Washington State University, Pullman, WA, United States
| | - Oleg A Zadvornyy
- Institute of Biological Chemistry, Washington State University, Pullman, WA, United States
| | - David W Mulder
- National Renewable Energy Laboratory, Biosciences Center, Golden, CO, United States
| | - Paul W King
- National Renewable Energy Laboratory, Biosciences Center, Golden, CO, United States
| | - John W Peters
- Institute of Biological Chemistry, Washington State University, Pullman, WA, United States.
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228
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Genome Analysis of Endomicrobium proavitum Suggests Loss and Gain of Relevant Functions during the Evolution of Intracellular Symbionts. Appl Environ Microbiol 2017. [PMID: 28646115 DOI: 10.1128/aem.00656-17] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bacterial endosymbionts of eukaryotes show progressive genome erosion, but detailed investigations of the evolutionary processes involved in the transition to an intracellular lifestyle are generally hampered by the lack of extant free-living lineages. Here, we characterize the genome of the recently isolated, free-living Endomicrobium proavitum, the second member of the Elusimicrobia phylum brought into pure culture, and compare it to the closely related "Candidatus Endomicrobium trichonymphae" strain Rs-D17, a previously described but uncultured endosymbiont of termite gut flagellates. A reconstruction of the metabolic pathways of Endomicrobium proavitum matched the fermentation products formed in pure culture and underscored its restriction to glucose as the substrate. However, several pathways present in the free-living strain, e.g., for the uptake and activation of glucose and its subsequent fermentation, ammonium assimilation, and outer membrane biogenesis, were absent or disrupted in the endosymbiont, probably lost during the massive genome rearrangements that occurred during symbiogenesis. While the majority of the genes in strain Rs-D17 have orthologs in Endomicrobium proavitum, the endosymbiont also possesses a number of functions that are absent from the free-living strain and may represent adaptations to the intracellular lifestyle. Phylogenetic analysis revealed that the genes encoding glucose 6-phosphate and amino acid transporters, acetaldehyde/alcohol dehydrogenase, and the pathways of glucuronic acid catabolism and thiamine pyrophosphate biosynthesis were either acquired by horizontal gene transfer or may represent ancestral traits that were lost in the free-living strain. The polyphyletic origin of Endomicrobia in different flagellate hosts makes them excellent models for future studies of convergent and parallel evolution during symbiogenesis.IMPORTANCE The isolation of a free-living relative of intracellular symbionts provides the rare opportunity to identify the evolutionary processes that occur in the course of symbiogenesis. Our study documents that the genome of "Candidatus Endomicrobium trichonymphae," which represents a clade of endosymbionts that have coevolved with termite gut flagellates for more than 40 million years, is not simply a subset of the genes present in Endomicrobium proavitum, a member of the ancestral, free-living lineage. Rather, comparative genomics revealed that the endosymbionts possess several relevant functions that were either prerequisites for colonization of the intracellular habitat or might have served to compensate for genes losses that occurred during genome erosion. Some gene sets found only in the endosymbiont were apparently acquired by horizontal transfer from other gut bacteria, which suggests that the intracellular bacteria of flagellates are not entirely cut off from gene flow.
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The dual-function chaperone HycH improves assembly of the formate hydrogenlyase complex. Biochem J 2017; 474:2937-2950. [PMID: 28718449 DOI: 10.1042/bcj20170431] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 07/11/2017] [Accepted: 07/17/2017] [Indexed: 11/17/2022]
Abstract
The assembly of multi-protein complexes requires the concerted synthesis and maturation of its components and subsequently their co-ordinated interaction. The membrane-bound formate hydrogenlyase (FHL) complex is the primary hydrogen-producing enzyme in Escherichia coli and is composed of seven subunits mostly encoded within the hycA-I operon for [NiFe]-hydrogenase-3 (Hyd-3). The HycH protein is predicted to have an accessory function and is not part of the final structural FHL complex. In this work, a mutant strain devoid of HycH was characterised and found to have significantly reduced FHL activity due to the instability of the electron transfer subunits. HycH was shown to interact specifically with the unprocessed species of HycE, the catalytic hydrogenase subunit of the FHL complex, at different stages during the maturation and assembly of the complex. Variants of HycH were generated with the aim of identifying interacting residues and those that influence activity. The R70/71/K72, the Y79, the E81 and the Y128 variant exchanges interrupt the interaction with HycE without influencing the FHL activity. In contrast, FHL activity, but not the interaction with HycE, was negatively influenced by H37 exchanges with polar residues. Finally, a HycH Y30 variant was unstable. Surprisingly, an overlapping function between HycH with its homologous counterpart HyfJ from the operon encoding [NiFe]-hydrogenase-4 (Hyd-4) was identified and this is the first example of sharing maturation machinery components between Hyd-3 and Hyd-4 complexes. The data presented here show that HycH has a novel dual role as an assembly chaperone for a cytoplasmic [NiFe]-hydrogenase.
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Organophosphorous ligands in hydrogenase-inspired iron-based catalysts: A DFT study on the energetics of metal protonation as a function of P-atom substitution. J PHYS ORG CHEM 2017. [DOI: 10.1002/poc.3748] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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231
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Mixotrophy drives niche expansion of verrucomicrobial methanotrophs. ISME JOURNAL 2017; 11:2599-2610. [PMID: 28777381 PMCID: PMC5649168 DOI: 10.1038/ismej.2017.112] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2016] [Revised: 04/07/2017] [Accepted: 05/12/2017] [Indexed: 01/26/2023]
Abstract
Aerobic methanotrophic bacteria have evolved a specialist lifestyle dependent on consumption of methane and other short-chain carbon compounds. However, their apparent substrate specialism runs contrary to the high relative abundance of these microorganisms in dynamic environments, where the availability of methane and oxygen fluctuates. In this work, we provide in situ and ex situ evidence that verrucomicrobial methanotrophs are mixotrophs. Verrucomicrobia-dominated soil communities from an acidic geothermal field in Rotokawa, New Zealand rapidly oxidised methane and hydrogen simultaneously. We isolated and characterised a verrucomicrobial strain from these soils, Methylacidiphilum sp. RTK17.1, and showed that it constitutively oxidises molecular hydrogen. Genomic analysis confirmed that this strain encoded two [NiFe]-hydrogenases (group 1d and 3b), and biochemical assays revealed that it used hydrogen as an electron donor for aerobic respiration and carbon fixation. While the strain could grow heterotrophically on methane or autotrophically on hydrogen, it grew optimally by combining these metabolic strategies. Hydrogen oxidation was particularly important for adaptation to methane and oxygen limitation. Complementary to recent findings of hydrogenotrophic growth by Methylacidiphilum fumariolicum SolV, our findings illustrate that verrucomicrobial methanotrophs have evolved to simultaneously utilise hydrogen and methane from geothermal sources to meet energy and carbon demands where nutrient flux is dynamic. This mixotrophic lifestyle is likely to have facilitated expansion of the niche space occupied by these microorganisms, allowing them to become dominant in geothermally influenced surface soils. Genes encoding putative oxygen-tolerant uptake [NiFe]-hydrogenases were identified in all publicly available methanotroph genomes, suggesting hydrogen oxidation is a general metabolic strategy in this guild.
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232
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Artz JH, Mulder DW, Ratzloff MW, Lubner CE, Zadvornyy OA, LeVan AX, Williams SG, Adams MWW, Jones AK, King PW, Peters JW. Reduction Potentials of [FeFe]-Hydrogenase Accessory Iron-Sulfur Clusters Provide Insights into the Energetics of Proton Reduction Catalysis. J Am Chem Soc 2017. [PMID: 28635269 DOI: 10.1021/jacs.7b02099] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
An [FeFe]-hydrogenase from Clostridium pasteurianum, CpI, is a model system for biological H2 activation. In addition to the catalytic H-cluster, CpI contains four accessory iron-sulfur [FeS] clusters in a branched series that transfer electrons to and from the active site. In this work, potentiometric titrations have been employed in combination with electron paramagnetic resonance (EPR) spectroscopy at defined electrochemical potentials to gain insights into the role of the accessory clusters in catalysis. EPR spectra collected over a range of potentials were deconvoluted into individual components attributable to the accessory [FeS] clusters and the active site H-cluster, and reduction potentials for each cluster were determined. The data suggest a large degree of magnetic coupling between the clusters. The distal [4Fe-4S] cluster is shown to have a lower reduction potential (∼ < -450 mV) than the other clusters, and molecular docking experiments indicate that the physiological electron donor, ferredoxin (Fd), most favorably interacts with this cluster. The low reduction potential of the distal [4Fe-4S] cluster thermodynamically restricts the Fdox/Fdred ratio at which CpI can operate, consistent with the role of CpI in recycling Fdred that accumulates during fermentation. Subsequent electron transfer through the additional accessory [FeS] clusters to the H-cluster is thermodynamically favorable.
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Affiliation(s)
- Jacob H Artz
- Institute of Biological Chemistry, Washington State University , 258 Clark Hall, Pullman, Washington 99163, United States
| | - David W Mulder
- Biosciences Center, National Renewable Energy Laboratory , 15013 Denver West Parkway, Golden, Colorado 80401, United States
| | - Michael W Ratzloff
- Biosciences Center, National Renewable Energy Laboratory , 15013 Denver West Parkway, Golden, Colorado 80401, United States
| | - Carolyn E Lubner
- Biosciences Center, National Renewable Energy Laboratory , 15013 Denver West Parkway, Golden, Colorado 80401, United States
| | - Oleg A Zadvornyy
- Institute of Biological Chemistry, Washington State University , 258 Clark Hall, Pullman, Washington 99163, United States
| | - Axl X LeVan
- Department of Chemistry and Biochemistry, Montana State University , 224 Chemistry and Biochemistry Building, Bozeman, Montana 59717, United States
| | - S Garrett Williams
- School of Molecular Sciences, Arizona State University , P.O. Box 871604, Tempe, Arizona 85287, United States
| | - Michael W W Adams
- B216B Life Sciences Complex, Department of Biochemistry, The University of Georgia , Athens, Georgia 30602, United States
| | - Anne K Jones
- School of Molecular Sciences, Arizona State University , P.O. Box 871604, Tempe, Arizona 85287, United States
| | - Paul W King
- Biosciences Center, National Renewable Energy Laboratory , 15013 Denver West Parkway, Golden, Colorado 80401, United States
| | - John W Peters
- Institute of Biological Chemistry, Washington State University , 258 Clark Hall, Pullman, Washington 99163, United States
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233
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Baba R, Morita M, Asakawa S, Watanabe T. Transcription of [FeFe]-Hydrogenase Genes during H 2 Production in Clostridium and Desulfovibrio spp. Isolated from a Paddy Field Soil. Microbes Environ 2017; 32:125-132. [PMID: 28502969 PMCID: PMC5478535 DOI: 10.1264/jsme2.me16171] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Changes in the relative abundances of the transcripts of hydA gene paralogs for [FeFe]-hydrogenase in Clostridium sp. strain H2 and Desulfovibrio sp. strain A1 isolated from paddy field soil were analyzed during H2 production. Strains H2 and A1 had at least five and two phylogenetically different hydA genes, respectively. The relative abundances of their hydA transcripts differed among the paralogs and H2 production activity changed in a manner that depended on the growth phase and conditions. Increases or decreases in the relative abundances of the transcripts of two out of five hydA genes in strain H2 correlated with changes in H2 production rates, whereas those of the others remained unchanged or decreased. In strain A1, the relative abundances of the transcripts of two hydA genes differed between monoculture, sulfate-reducing, and syntrophic, methanogenic conditions. The relative abundance of the transcripts of one hydA gene, predicted to encode a cytosolic [FeFe]-hydrogenase, was higher under syntrophic, methanogenic conditions than sulfate-reducing conditions, while that of the transcripts of the other hydA gene decreased with time under both conditions. This study showed that the transcription of the hydA gene during growth with active H2 production was differently regulated among the paralogs in H2 producers isolated from paddy field soil.
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Affiliation(s)
- Ryuko Baba
- Laboratory of Soil Biology and Chemistry, Department of Biological Mechanisms and Functions, Graduate School of Bioagricultural Sciences, Nagoya University
| | - Mayumi Morita
- Laboratory of Soil Biology and Chemistry, School of Agricultural Sciences, Nagoya University
| | - Susumu Asakawa
- Laboratory of Soil Biology and Chemistry, Department of Biological Mechanisms and Functions, Graduate School of Bioagricultural Sciences, Nagoya University
| | - Takeshi Watanabe
- Laboratory of Soil Biology and Chemistry, Department of Biological Mechanisms and Functions, Graduate School of Bioagricultural Sciences, Nagoya University
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234
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Shepard EM, Byer AS, Aggarwal P, Betz JN, Scott AG, Shisler KA, Usselman RJ, Eaton GR, Eaton SS, Broderick JB. Electron Spin Relaxation and Biochemical Characterization of the Hydrogenase Maturase HydF: Insights into [2Fe-2S] and [4Fe-4S] Cluster Communication and Hydrogenase Activation. Biochemistry 2017; 56:3234-3247. [PMID: 28525271 PMCID: PMC5490485 DOI: 10.1021/acs.biochem.7b00169] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Nature utilizes [FeFe]-hydrogenase enzymes to catalyze the interconversion between H2 and protons and electrons. Catalysis occurs at the H-cluster, a carbon monoxide-, cyanide-, and dithiomethylamine-coordinated 2Fe subcluster bridged via a cysteine to a [4Fe-4S] cluster. Biosynthesis of this unique metallocofactor is accomplished by three maturase enzymes denoted HydE, HydF, and HydG. HydE and HydG belong to the radical S-adenosylmethionine superfamily of enzymes and synthesize the nonprotein ligands of the H-cluster. These enzymes interact with HydF, a GTPase that acts as a scaffold or carrier protein during 2Fe subcluster assembly. Prior characterization of HydF demonstrated the protein exists in both dimeric and tetrameric states and coordinates both [4Fe-4S]2+/+ and [2Fe-2S]2+/+ clusters [Shepard, E. M., Byer, A. S., Betz, J. N., Peters, J. W., and Broderick, J. B. (2016) Biochemistry 55, 3514-3527]. Herein, electron paramagnetic resonance (EPR) is utilized to characterize the [2Fe-2S]+ and [4Fe-4S]+ clusters bound to HydF. Examination of spin relaxation times using pulsed EPR in HydF samples exhibiting both [4Fe-4S]+ and [2Fe-2S]+ cluster EPR signals supports a model in which the two cluster types either are bound to widely separated sites on HydF or are not simultaneously bound to a single HydF species. Gel filtration chromatographic analyses of HydF spectroscopic samples strongly suggest the [2Fe-2S]+ and [4Fe-4S]+ clusters are coordinated to the dimeric form of the protein. Lastly, we examined the 2Fe subcluster-loaded form of HydF and showed the dimeric state is responsible for [FeFe]-hydrogenase activation. Together, the results indicate a specific role for the HydF dimer in the H-cluster biosynthesis pathway.
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Affiliation(s)
- Eric M Shepard
- Department of Chemistry and Biochemistry, Montana State University , Bozeman, Montana 59717, United States
| | - Amanda S Byer
- Department of Chemistry and Biochemistry, Montana State University , Bozeman, Montana 59717, United States
| | - Priyanka Aggarwal
- Department of Chemistry and Biochemistry, University of Denver , Denver, Colorado 80208, United States
| | - Jeremiah N Betz
- Department of Chemistry and Biochemistry, Montana State University , Bozeman, Montana 59717, United States
| | - Anna G Scott
- Department of Chemistry and Biochemistry, Montana State University , Bozeman, Montana 59717, United States
| | - Krista A Shisler
- Department of Chemistry and Biochemistry, Montana State University , Bozeman, Montana 59717, United States
| | - Robert J Usselman
- Department of Chemistry and Biochemistry, Montana State University , Bozeman, Montana 59717, United States
| | - Gareth R Eaton
- Department of Chemistry and Biochemistry, University of Denver , Denver, Colorado 80208, United States
| | - Sandra S Eaton
- Department of Chemistry and Biochemistry, University of Denver , Denver, Colorado 80208, United States
| | - Joan B Broderick
- Department of Chemistry and Biochemistry, Montana State University , Bozeman, Montana 59717, United States
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235
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Pohorille A, Wilson MA, Shannon G. Flexible Proteins at the Origin of Life. Life (Basel) 2017; 7:E23. [PMID: 28587235 PMCID: PMC5492145 DOI: 10.3390/life7020023] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Revised: 05/10/2017] [Accepted: 05/24/2017] [Indexed: 11/17/2022] Open
Abstract
Almost all modern proteins possess well-defined, relatively rigid scaffolds that provide structural preorganization for desired functions. Such scaffolds require the sufficient length of a polypeptide chain and extensive evolutionary optimization. How ancestral proteins attained functionality, even though they were most likely markedly smaller than their contemporary descendants, remains a major, unresolved question in the origin of life. On the basis of evidence from experiments and computer simulations, we argue that at least some of the earliest water-soluble and membrane proteins were markedly more flexible than their modern counterparts. As an example, we consider a small, evolved in vitro ligase, based on a novel architecture that may be the archetype of primordial enzymes. The protein does not contain a hydrophobic core or conventional elements of the secondary structure characteristic of modern water-soluble proteins, but instead is built of a flexible, catalytic loop supported by a small hydrophilic core containing zinc atoms. It appears that disorder in the polypeptide chain imparts robustness to mutations in the protein core. Simple ion channels, likely the earliest membrane protein assemblies, could also be quite flexible, but still retain their functionality, again in contrast to their modern descendants. This is demonstrated in the example of antiamoebin, which can serve as a useful model of small peptides forming ancestral ion channels. Common features of the earliest, functional protein architectures discussed here include not only their flexibility, but also a low level of evolutionary optimization and heterogeneity in amino acid composition and, possibly, the type of peptide bonds in the protein backbone.
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Affiliation(s)
- Andrew Pohorille
- Exobiology Branch, MS 239-4, NASA Ames Research Center, Moffett Field, CA 94035, USA.
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94132, USA.
| | - Michael A Wilson
- Exobiology Branch, MS 239-4, NASA Ames Research Center, Moffett Field, CA 94035, USA.
- SETI Institute, 189 N Bernardo Ave #200, Mountain View, CA 94043, USA.
| | - Gareth Shannon
- Exobiology Branch, MS 239-4, NASA Ames Research Center, Moffett Field, CA 94035, USA.
- NASA Postdoctoral Program Fellow, NASA Ames Research Center, Moffett Field, CA 94035, USA.
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236
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Schink B, Montag D, Keller A, Müller N. Hydrogen or formate: Alternative key players in methanogenic degradation. ENVIRONMENTAL MICROBIOLOGY REPORTS 2017; 9:189-202. [PMID: 28205388 DOI: 10.1111/1758-2229.12524] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Hydrogen and formate are important electron carriers in methanogenic degradation in anoxic environments such as sediments, sewage sludge digestors and biogas reactors. Especially in the terminal steps of methanogenesis, they determine the energy budgets of secondary (syntrophically) fermenting bacteria and their methanogenic partners. The literature provides considerable data on hydrogen pool sizes in such habitats, but little data exist for formate concentrations due to technical difficulties in formate determination at low concentration. Recent evidence from biochemical and molecular biological studies indicates that several secondary fermenters can use both hydrogen and formate for electron release, and may do so even simultaneously. Numerous strictly anaerobic bacteria contain enzymes which equilibrate hydrogen and formate pools to energetically equal values, and recent measurements in sewage digestors and biogas reactors indicate that - beyond occasional fluctuations - the pool sizes of hydrogen and formate are indeed energetically nearly equivalent. Nonetheless, a thermophilic archaeon from a submarine hydrothermal vent, Thermococcus onnurineus, can obtain ATP from the conversion of formate to hydrogen plus bicarbonate at 80°C, indicating that at least in this extreme environment the pools of formate and hydrogen are likely to be sufficiently different to support such an unusual type of energy conservation.
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Affiliation(s)
- Bernhard Schink
- Department of Biology, Microbial Ecology, University of Konstanz, Konstanz, D-78457, Germany
| | - Dominik Montag
- Department of Biology, Microbial Ecology, University of Konstanz, Konstanz, D-78457, Germany
| | - Anja Keller
- Department of Biology, Microbial Ecology, University of Konstanz, Konstanz, D-78457, Germany
| | - Nicolai Müller
- Department of Biology, Microbial Ecology, University of Konstanz, Konstanz, D-78457, Germany
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237
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Carr CE, Musiani F, Huang HT, Chivers PT, Ciurli S, Maroney MJ. Glutamate Ligation in the Ni(II)- and Co(II)-Responsive Escherichia coli Transcriptional Regulator, RcnR. Inorg Chem 2017; 56:6459-6476. [PMID: 28517938 DOI: 10.1021/acs.inorgchem.7b00527] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Escherichia coli RcnR (resistance to cobalt and nickel regulator, EcRcnR) is a metal-responsive repressor of the genes encoding the Ni(II) and Co(II) exporter proteins RcnAB by binding to PRcnAB. The DNA binding affinity is weakened when the cognate ions Ni(II) and Co(II) bind to EcRcnR in a six-coordinate site that features a (N/O)5S ligand donor-atom set in distinct sites: while both metal ions are bound by the N terminus, Cys35, and His64, Co(II) is additionally bound by His3. On the other hand, the noncognate Zn(II) and Cu(I) ions feature a lower coordination number, have a solvent-accessible binding site, and coordinate protein ligands that do not include the N-terminal amine. A molecular model of apo-EcRcnR suggested potential roles for Glu34 and Glu63 in binding Ni(II) and Co(II) to EcRcnR. The roles of Glu34 and Glu63 in metal binding, metal selectivity, and function were therefore investigated using a structure/function approach. X-ray absorption spectroscopy was used to assess the structural changes in the Ni(II), Co(II), and Zn(II) binding sites of Glu → Ala and Glu → Cys variants at both positions. The effect of these structural alterations on the regulation of PrcnA by EcRcnR in response to metal binding was explored using LacZ reporter assays. These combined studies indicate that while Glu63 is a ligand for both metal ions, Glu34 is a ligand for Co(II) but possibly not for Ni(II). The Glu34 variants affect the structure of the cognate metal sites, but they have no effect on the transcriptional response. In contrast, the Glu63 variants affect both the structure and transcriptional response, although they do not completely abolish the function of EcRcnR. The structure of the Zn(II) site is not significantly perturbed by any of the glutamic acid variations. The spectroscopic and functional data obtained on the mutants were used to calculate models of the metal-site structures of EcRcnR bound to Ni(II), Co(II), and Zn(II). The results are interpreted in terms of a switch mechanism, in which a subset of the metal-binding ligands is responsible for the allosteric response required for DNA release.
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Affiliation(s)
- Carolyn E Carr
- Department of Chemistry, University of Massachusetts , Amherst, Massachusetts 01003, United States
| | - Francesco Musiani
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna , Bologna 40126, Italy
| | - Hsin-Ting Huang
- Department of Chemistry, University of Massachusetts , Amherst, Massachusetts 01003, United States
| | - Peter T Chivers
- Departments of Biosciences and Chemistry, Durham University , Durham DH1 3LE, United Kingdom
| | - Stefano Ciurli
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna , Bologna 40126, Italy
| | - Michael J Maroney
- Department of Chemistry, University of Massachusetts , Amherst, Massachusetts 01003, United States
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238
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Galazzo L, Maso L, De Rosa E, Bortolus M, Doni D, Acquasaliente L, De Filippis V, Costantini P, Carbonera D. Identifying conformational changes with site-directed spin labeling reveals that the GTPase domain of HydF is a molecular switch. Sci Rep 2017; 7:1714. [PMID: 28490758 PMCID: PMC5431965 DOI: 10.1038/s41598-017-01886-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Accepted: 04/05/2017] [Indexed: 11/17/2022] Open
Abstract
[FeFe]-hydrogenases catalyse the reduction of protons to hydrogen at a complex 2Fe[4Fe4S] center called H-cluster. The assembly of this active site is a multistep process involving three proteins, HydE, HydF and HydG. According to the current models, HydF has the key double role of scaffold, upon which the final H-cluster precursor is assembled, and carrier to transfer it to the target hydrogenase. The X-ray structure of HydF indicates that the protein is a homodimer with both monomers carrying two functional domains: a C-terminal FeS cluster-binding domain, where the precursor is assembled, and a N-terminal GTPase domain, whose exact contribution to cluster biogenesis and hydrogenase activation is still elusive. We previously obtained several hints suggesting that the binding of GTP to HydF could be involved in the interactions of this scaffold protein with the other maturases and with the hydrogenase itself. In this work, by means of site directed spin labeling coupled to EPR/PELDOR spectroscopy, we explored the conformational changes induced in a recombinant HydF protein by GTP binding, and provide the first clue that the HydF GTPase domain could be involved in the H-cluster assembly working as a molecular switch similarly to other known small GTPases.
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Affiliation(s)
- Laura Galazzo
- Department of Chemical Sciences, University of Padova, Via F. Marzolo 1, 35131, Padova, Italy
| | - Lorenzo Maso
- Department of Biology, University of Padova, Viale G. Colombo 3, 35131, Padova, Italy
| | - Edith De Rosa
- Department of Biology, University of Padova, Viale G. Colombo 3, 35131, Padova, Italy
| | - Marco Bortolus
- Department of Chemical Sciences, University of Padova, Via F. Marzolo 1, 35131, Padova, Italy
| | - Davide Doni
- Department of Chemical Sciences, University of Padova, Via F. Marzolo 1, 35131, Padova, Italy
| | - Laura Acquasaliente
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Via F. Marzolo 5, 35131, Padova, Italy
| | - Vincenzo De Filippis
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Via F. Marzolo 5, 35131, Padova, Italy
| | - Paola Costantini
- Department of Biology, University of Padova, Viale G. Colombo 3, 35131, Padova, Italy.
| | - Donatella Carbonera
- Department of Chemical Sciences, University of Padova, Via F. Marzolo 1, 35131, Padova, Italy.
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239
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Zanello P. The competition between chemistry and biology in assembling iron–sulfur derivatives. Molecular structures and electrochemistry. Part V. {[Fe4S4](SCysγ)4} proteins. Coord Chem Rev 2017. [DOI: 10.1016/j.ccr.2016.10.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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240
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Nagarajan D, Lee DJ, Kondo A, Chang JS. Recent insights into biohydrogen production by microalgae - From biophotolysis to dark fermentation. BIORESOURCE TECHNOLOGY 2017; 227:373-387. [PMID: 28089136 DOI: 10.1016/j.biortech.2016.12.104] [Citation(s) in RCA: 89] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Revised: 12/24/2016] [Accepted: 12/27/2016] [Indexed: 06/06/2023]
Abstract
One of the best options to alleviate the problems associated with global warming and climate change is to reduce burning of fossil fuels and search for new alternative energy resources. In case of biodiesel and bioethanol production, the choice of feedstock and the process design influences the GHG emissions and appropriate methods need to be adapted. Hydrogen is a zero-carbon and energy dense alternative energy carrier with clean burning properties and biohydrogen production by microalgae can reduce production associated GHG emissions to a great extent. Biohydrogen can be produced through dark fermentation using sugars, starch, or cellulosic materials. Microalgae-based biohydrogen production is recently regarded as a promising pathway for biohydrogen production via photolysis or being a substrate for anaerobic fermentation. This review lists the methods of hydrogen production by microalgae. The enzymes involved and the factors affecting the biohydrogen production process are discussed. The bottlenecks in microalgae-based biohydrogen production are critically reviewed and future research areas in hydrogen production are presented.
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Affiliation(s)
- Dillirani Nagarajan
- Department of Chemical Engineering, National Cheng Kung University, Tainan, Taiwan; Department of Chemical Engineering, National Taiwan University, Taipei, Taiwan
| | - Duu-Jong Lee
- Department of Chemical Engineering, National Taiwan University, Taipei, Taiwan
| | - Akihiko Kondo
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodai, Nada-ku, Kobe 657-8501, Japan; Core Research for Evolutional Science and Technology, Japan Science and Technology Agency, 3-5 Sanbancho, Chiyoda-ku, Tokyo 102-0075, Japan; Biomass Engineering Program, RIKEN, 1-7-22 Suehiro, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Jo-Shu Chang
- Department of Chemical Engineering, National Cheng Kung University, Tainan, Taiwan; Research Center for Energy Technology and Strategy, National Cheng Kung University, Tainan, Taiwan.
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241
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Reddy K, Nasr M, Kumari S, Kumar S, Gupta SK, Enitan AM, Bux F. Biohydrogen production from sugarcane bagasse hydrolysate: effects of pH, S/X, Fe 2+, and magnetite nanoparticles. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2017; 24:8790-8804. [PMID: 28213710 DOI: 10.1007/s11356-017-8560-1] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 02/02/2017] [Indexed: 06/06/2023]
Abstract
Batch dark fermentation experiments were conducted to investigate the effects of initial pH, substrate-to-biomass (S/X) ratio, and concentrations of Fe2+ and magnetite nanoparticles on biohydrogen production from sugarcane bagasse (SCB) hydrolysate. By applying the response surface methodology, the optimum condition of steam-acid hydrolysis was 0.64% (v/v) H2SO4 for 55.7 min, which obtained a sugar yield of 274 mg g-1. The maximum hydrogen yield (HY) of 0.874 mol (mol glucose-1) was detected at the optimum pH of 5.0 and S/X ratio of 0.5 g chemical oxygen demand (COD, g VSS-1). The addition of Fe2+ 200 mg L-1 and magnetite nanoparticles 200 mg L-1 to the inoculum enhanced the HY by 62.1% and 69.6%, respectively. The kinetics of hydrogen production was estimated by fitting the experimental data to the modified Gompertz model. The inhibitory effects of adding Fe2+ and magnetite nanoparticles to the fermentative hydrogen production were examined by applying Andrew's inhibition model. COD mass balance and full stoichiometric reactions, including soluble metabolic products, cell synthesis, and H2 production, indicated the reliability of the experimental results. A qPCR-based analysis was conducted to assess the microbial community structure using Enterobacteriaceae, Clostridium spp., and hydrogenase-specific gene activity. Results from the microbial analysis revealed the dominance of hydrogen producers in the inoculum immobilized on magnetite nanoparticles, followed by the inoculum supplemented with Fe2+ concentration. Graphical abstract ᅟ.
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Affiliation(s)
- Karen Reddy
- Institute for Water and Wastewater Technology, Durban University of Technology, Durban, 4000, South Africa
| | - Mahmoud Nasr
- Sanitary Engineering Department, Faculty of Engineering, Alexandria University, Alexandria, 21544, Egypt
| | - Sheena Kumari
- Institute for Water and Wastewater Technology, Durban University of Technology, Durban, 4000, South Africa
| | - Santhosh Kumar
- Department of Biotechnology and Food Technology, Durban University of Technology, Durban, 4000, South Africa
| | - Sanjay Kumar Gupta
- Institute for Water and Wastewater Technology, Durban University of Technology, Durban, 4000, South Africa
| | - Abimbola Motunrayo Enitan
- Institute for Water and Wastewater Technology, Durban University of Technology, Durban, 4000, South Africa
| | - Faizal Bux
- Institute for Water and Wastewater Technology, Durban University of Technology, Durban, 4000, South Africa.
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242
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Kublanov IV, Sigalova OM, Gavrilov SN, Lebedinsky AV, Rinke C, Kovaleva O, Chernyh NA, Ivanova N, Daum C, Reddy TBK, Klenk HP, Spring S, Göker M, Reva ON, Miroshnichenko ML, Kyrpides NC, Woyke T, Gelfand MS, Bonch-Osmolovskaya EA. Genomic Analysis of Caldithrix abyssi, the Thermophilic Anaerobic Bacterium of the Novel Bacterial Phylum Calditrichaeota. Front Microbiol 2017; 8:195. [PMID: 28265262 PMCID: PMC5317091 DOI: 10.3389/fmicb.2017.00195] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2016] [Accepted: 01/26/2017] [Indexed: 11/13/2022] Open
Abstract
The genome of Caldithrix abyssi, the first cultivated representative of a phylum-level bacterial lineage, was sequenced within the framework of Genomic Encyclopedia of Bacteria and Archaea (GEBA) project. The genomic analysis revealed mechanisms allowing this anaerobic bacterium to ferment peptides or to implement nitrate reduction with acetate or molecular hydrogen as electron donors. The genome encoded five different [NiFe]- and [FeFe]-hydrogenases, one of which, group 1 [NiFe]-hydrogenase, is presumably involved in lithoheterotrophic growth, three other produce H2 during fermentation, and one is apparently bidirectional. The ability to reduce nitrate is determined by a nitrate reductase of the Nap family, while nitrite reduction to ammonia is presumably catalyzed by an octaheme cytochrome c nitrite reductase εHao. The genome contained genes of respiratory polysulfide/thiosulfate reductase, however, elemental sulfur and thiosulfate were not used as the electron acceptors for anaerobic respiration with acetate or H2, probably due to the lack of the gene of the maturation protein. Nevertheless, elemental sulfur and thiosulfate stimulated growth on fermentable substrates (peptides), being reduced to sulfide, most probably through the action of the cytoplasmic sulfide dehydrogenase and/or NAD(P)-dependent [NiFe]-hydrogenase (sulfhydrogenase) encoded by the genome. Surprisingly, the genome of this anaerobic microorganism encoded all genes for cytochrome c oxidase, however, its maturation machinery seems to be non-operational due to genomic rearrangements of supplementary genes. Despite the fact that sugars were not among the substrates reported when C. abyssi was first described, our genomic analysis revealed multiple genes of glycoside hydrolases, and some of them were predicted to be secreted. This finding aided in bringing out four carbohydrates that supported the growth of C. abyssi: starch, cellobiose, glucomannan and xyloglucan. The genomic analysis demonstrated the ability of C. abyssi to synthesize nucleotides and most amino acids and vitamins. Finally, the genomic sequence allowed us to perform a phylogenomic analysis, based on 38 protein sequences, which confirmed the deep branching of this lineage and justified the proposal of a novel phylum Calditrichaeota.
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Affiliation(s)
- Ilya V Kublanov
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences Moscow, Russia
| | - Olga M Sigalova
- A.A.Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences Moscow, Russia
| | - Sergey N Gavrilov
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences Moscow, Russia
| | - Alexander V Lebedinsky
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences Moscow, Russia
| | - Christian Rinke
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia QLD, Australia
| | - Olga Kovaleva
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences Moscow, Russia
| | - Nikolai A Chernyh
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences Moscow, Russia
| | | | - Chris Daum
- DOE Joint Genome Institute, Walnut Creek CA, USA
| | - T B K Reddy
- DOE Joint Genome Institute, Walnut Creek CA, USA
| | | | - Stefan Spring
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures Braunschweig, Germany
| | - Markus Göker
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures Braunschweig, Germany
| | - Oleg N Reva
- Center for Bioinformatics and Computational Biology, Department of Biochemistry, University of Pretoria Pretoria, South Africa
| | - Margarita L Miroshnichenko
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences Moscow, Russia
| | | | - Tanja Woyke
- DOE Joint Genome Institute, Walnut CreekCA, USA; Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, BerkeleyCA, USA
| | - Mikhail S Gelfand
- A.A.Kharkevich Institute for Information Transmission Problems, Russian Academy of SciencesMoscow, Russia; Department of Bioengineering and Bioinformatics, M.V. Lomonosov Moscow State UniversityMoscow, Russia; Skolkovo Institute of Science and TechnologyMoscow, Russia; Faculty of Computer Science, National Research University - Higher School of EconomicsMoscow, Russia
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243
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Zeer-Wanklyn CJ, Zamble DB. Microbial nickel: cellular uptake and delivery to enzyme centers. Curr Opin Chem Biol 2017; 37:80-88. [PMID: 28213182 DOI: 10.1016/j.cbpa.2017.01.014] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Revised: 01/12/2017] [Accepted: 01/18/2017] [Indexed: 01/29/2023]
Abstract
Nickel enzymes allow microorganisms to access chemistry that can be vital for survival and virulence. In this review we highlight recent work on several systems that import nickel ions and deliver them to the active sites of these enzymes. Small molecules, in particular l-His and derivatives, may chelate nickel ions before import at TonB-dependent outer-membrane and ABC-type inner-membrane transporters. Inside the cell, nickel ions are used by maturation factors required to produce nickel enzymes such as [NiFe]-hydrogenase, urease and lactate racemase. These accessory proteins often exhibit metal selectivity and frequently include an NTP-hydrolyzing metallochaperone protein. The research described provides a deeper understanding of the processes that allow microorganisms to access nickel ions from the environment and incorporate them into nickel proteins.
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Affiliation(s)
- Conor J Zeer-Wanklyn
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
| | - Deborah B Zamble
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6, Canada.
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244
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Lorion MM, Maindan K, Kapdi AR, Ackermann L. Heteromultimetallic catalysis for sustainable organic syntheses. Chem Soc Rev 2017; 46:7399-7420. [DOI: 10.1039/c6cs00787b] [Citation(s) in RCA: 113] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Fully complementary bimetallic catalysis has been identified as an increasingly powerful tool for molecular transformations, which was largely inspired by early examples of sequential catalytic transformations.
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Affiliation(s)
- Mélanie M. Lorion
- Institut fur Organische und Biomolekulare Chemie
- Georg-August-Universität
- 37077 Göttingen
- Germany
| | - Karan Maindan
- Department of Chemistry
- Institute of Chemical Technology
- Mumbai-400019
- India
| | - Anant R. Kapdi
- Department of Chemistry
- Institute of Chemical Technology
- Mumbai-400019
- India
| | - Lutz Ackermann
- Institut fur Organische und Biomolekulare Chemie
- Georg-August-Universität
- 37077 Göttingen
- Germany
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245
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Puggioni V, Tempel S, Latifi A. Distribution of Hydrogenases in Cyanobacteria: A Phylum-Wide Genomic Survey. Front Genet 2016; 7:223. [PMID: 28083017 PMCID: PMC5186783 DOI: 10.3389/fgene.2016.00223] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2016] [Accepted: 12/13/2016] [Indexed: 01/02/2023] Open
Abstract
Microbial Molecular hydrogen (H2) cycling plays an important role in several ecological niches. Hydrogenases (H2ases), enzymes involved in H2 metabolism, are of great interest for investigating microbial communities, and producing BioH2. To obtain an overall picture of the genetic ability of Cyanobacteria to produce H2ases, we conducted a phylum wide analysis of the distribution of the genes encoding these enzymes in 130 cyanobacterial genomes. The concomitant presence of the H2ase and genes involved in the maturation process, and that of well-conserved catalytic sites in the enzymes were the three minimal criteria used to classify a strain as being able to produce a functional H2ase. The [NiFe] H2ases were found to be the only enzymes present in this phylum. Fifty-five strains were found to be potentially able produce the bidirectional Hox enzyme and 33 to produce the uptake (Hup) enzyme. H2 metabolism in Cyanobacteria has a broad ecological distribution, since only the genomes of strains collected from the open ocean do not possess hox genes. In addition, the presence of H2ase was found to increase in the late branching clades of the phylogenetic tree of the species. Surprisingly, five cyanobacterial genomes were found to possess homologs of oxygen tolerant H2ases belonging to groups 1, 3b, and 3d. Overall, these data show that H2ases are widely distributed, and are therefore probably of great functional importance in Cyanobacteria. The present finding that homologs to oxygen-tolerant H2ases are present in this phylum opens new perspectives for applying the process of photosynthesis in the field of H2 production.
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Affiliation(s)
- Vincenzo Puggioni
- Laboratoire de Chimie Bactérienne UMR 7283, Centre National de la Recherche Scientifique (CNRS), Aix-Marseille University Marseille, France
| | - Sébastien Tempel
- Laboratoire de Chimie Bactérienne UMR 7283, Centre National de la Recherche Scientifique (CNRS), Aix-Marseille University Marseille, France
| | - Amel Latifi
- Laboratoire de Chimie Bactérienne UMR 7283, Centre National de la Recherche Scientifique (CNRS), Aix-Marseille University Marseille, France
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246
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Morra S, Valetti F, Gilardi G. [FeFe]-hydrogenases as biocatalysts in bio-hydrogen production. RENDICONTI LINCEI 2016. [DOI: 10.1007/s12210-016-0584-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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247
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van Lingen HJ, Plugge CM, Fadel JG, Kebreab E, Bannink A, Dijkstra J. Thermodynamic Driving Force of Hydrogen on Rumen Microbial Metabolism: A Theoretical Investigation. PLoS One 2016; 11:e0161362. [PMID: 27783615 PMCID: PMC5081179 DOI: 10.1371/journal.pone.0161362] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 08/04/2016] [Indexed: 01/26/2023] Open
Abstract
Hydrogen is a key product of rumen fermentation and has been suggested to thermodynamically control the production of the various volatile fatty acids (VFA). Previous studies, however, have not accounted for the fact that only thermodynamic near-equilibrium conditions control the magnitude of reaction rate. Furthermore, the role of NAD, which is affected by hydrogen partial pressure (PH2), has often not been considered. The aim of this study was to quantify the control of PH2 on reaction rates of specific fermentation pathways, methanogenesis and NADH oxidation in rumen microbes. The control of PH2 was quantified using the thermodynamic potential factor (FT), which is a dimensionless factor that corrects a predicted kinetic reaction rate for the thermodynamic control exerted. Unity FT was calculated for all glucose fermentation pathways considered, indicating no inhibition of PH2 on the production of a specific type of VFA (e.g., acetate, propionate and butyrate) in the rumen. For NADH oxidation without ferredoxin oxidation, increasing PH2 within the rumen physiological range decreased FT from unity to zero for different NAD+ to NADH ratios and pH of 6.2 and 7.0, which indicates thermodynamic control of PH2. For NADH oxidation with ferredoxin oxidation, increasing PH2 within the rumen physiological range decreased FT from unity at pH of 7.0 only. For the acetate to propionate conversion, FT increased from 0.65 to unity with increasing PH2, which indicates thermodynamic control. For propionate to acetate and butyrate to acetate conversions, FT decreased to zero below the rumen range of PH2, indicating full thermodynamic suppression. For methanogenesis by archaea without cytochromes, FT differed from unity only below the rumen range of PH2, indicating no thermodynamic control. This theoretical investigation shows that thermodynamic control of PH2 on individual VFA produced and associated yield of hydrogen and methane cannot be explained without considering NADH oxidation.
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Affiliation(s)
- Henk J. van Lingen
- TI Food and Nutrition, Wageningen, The Netherlands
- Animal Nutrition Group, Wageningen University, Wageningen, The Netherlands
- * E-mail:
| | - Caroline M. Plugge
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
| | - James G. Fadel
- Department of Animal Sciences, University of California, Davis, Davis, California, United States of America
| | - Ermias Kebreab
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
| | - André Bannink
- Animal Nutrition, Wageningen UR Livestock Research, Wageningen, the Netherlands
| | - Jan Dijkstra
- Animal Nutrition Group, Wageningen University, Wageningen, The Netherlands
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248
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Morra S, Arizzi M, Valetti F, Gilardi G. Oxygen Stability in the New [FeFe]-Hydrogenase from Clostridium beijerinckii SM10 (CbA5H). Biochemistry 2016; 55:5897-5900. [DOI: 10.1021/acs.biochem.6b00780] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Simone Morra
- Department of Life Sciences
and Systems Biology, University of Torino, Via Accademia Albertina 13, Torino 10123, Italy
| | - Mariaconcetta Arizzi
- Department of Life Sciences
and Systems Biology, University of Torino, Via Accademia Albertina 13, Torino 10123, Italy
| | - Francesca Valetti
- Department of Life Sciences
and Systems Biology, University of Torino, Via Accademia Albertina 13, Torino 10123, Italy
| | - Gianfranco Gilardi
- Department of Life Sciences
and Systems Biology, University of Torino, Via Accademia Albertina 13, Torino 10123, Italy
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249
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Baba R, Asakawa S, Watanabe T. H2-Producing Bacterial Community during Rice Straw Decomposition in Paddy Field Soil: Estimation by an Analysis of [FeFe]-Hydrogenase Gene Transcripts. Microbes Environ 2016; 31:226-33. [PMID: 27319579 PMCID: PMC5017798 DOI: 10.1264/jsme2.me16036] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Accepted: 04/30/2016] [Indexed: 11/29/2022] Open
Abstract
The transcription patterns of [FeFe]-hydrogenase genes (hydA), which encode the enzymes responsible for H2 production, were investigated during rice straw decomposition in paddy soil using molecular biological techniques. Paddy soil amended with and without rice straw was incubated under anoxic conditions. RNA was extracted from the soil, and three clone libraries of hydA were constructed using RNAs obtained from samples in the initial phase of rice straw decomposition (day 1 with rice straw), methanogenic phase of rice straw decomposition (day 14 with rice straw), and under a non-amended condition (day 14 without rice straw). hydA genes related to Proteobacteria, Firmicutes, Bacteroidetes, Chloroflexi, and Thermotogae were mainly transcribed in paddy soil samples; however, their proportions markedly differed among the libraries. Deltaproteobacteria-related hydA genes were predominantly transcribed on day 1 with rice straw, while various types of hydA genes related to several phyla were transcribed on day 14 with rice straw. Although the diversity of transcribed hydA was significantly higher in the library on day 14 with rice straw than the other two libraries, the composition of hydA transcripts in the library was similar to that in the library on day 14 without rice straw. These results indicate that the composition of active H2 producers and/or H2 metabolic patterns dynamically change during rice straw decomposition in paddy soil.
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Affiliation(s)
- Ryuko Baba
- Laboratory of Soil Biology and Chemistry, Department of Biological Mechanisms and Functions, Graduate School of Bioagricultural Sciences, Nagoya UniversityFurocho, Chikusa, Nagoya 464–8601Japan
| | - Susumu Asakawa
- Laboratory of Soil Biology and Chemistry, Department of Biological Mechanisms and Functions, Graduate School of Bioagricultural Sciences, Nagoya UniversityFurocho, Chikusa, Nagoya 464–8601Japan
| | - Takeshi Watanabe
- Laboratory of Soil Biology and Chemistry, Department of Biological Mechanisms and Functions, Graduate School of Bioagricultural Sciences, Nagoya UniversityFurocho, Chikusa, Nagoya 464–8601Japan
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250
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Søndergaard D, Pedersen CNS, Greening C. HydDB: A web tool for hydrogenase classification and analysis. Sci Rep 2016; 6:34212. [PMID: 27670643 PMCID: PMC5037454 DOI: 10.1038/srep34212] [Citation(s) in RCA: 300] [Impact Index Per Article: 37.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Accepted: 09/09/2016] [Indexed: 01/22/2023] Open
Abstract
H2 metabolism is proposed to be the most ancient and diverse mechanism of energy-conservation. The metalloenzymes mediating this metabolism, hydrogenases, are encoded by over 60 microbial phyla and are present in all major ecosystems. We developed a classification system and web tool, HydDB, for the structural and functional analysis of these enzymes. We show that hydrogenase function can be predicted by primary sequence alone using an expanded classification scheme (comprising 29 [NiFe], 8 [FeFe], and 1 [Fe] hydrogenase classes) that defines 11 new classes with distinct biological functions. Using this scheme, we built a web tool that rapidly and reliably classifies hydrogenase primary sequences using a combination of k-nearest neighbors' algorithms and CDD referencing. Demonstrating its capacity, the tool reliably predicted hydrogenase content and function in 12 newly-sequenced bacteria, archaea, and eukaryotes. HydDB provides the capacity to browse the amino acid sequences of 3248 annotated hydrogenase catalytic subunits and also contains a detailed repository of physiological, biochemical, and structural information about the 38 hydrogenase classes defined here. The database and classifier are freely and publicly available at http://services.birc.au.dk/hyddb/.
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Affiliation(s)
- Dan Søndergaard
- Aarhus University, Bioinformatics Research Centre, C.F. Møllers Allé 8, Aarhus DK-8000, Denmark
| | | | - Chris Greening
- The Commonwealth Scientific and Industrial Research Organisation, Land and Water Flagship, Clunies Ross Street, Acton, ACT 2601, Australia
- Monash University, School of Biological Sciences, Clayton, VIC 3800, Australia
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