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Opel F, Itzenhäuser MA, Wehner I, Lupacchini S, Lauterbach L, Lenz O, Klähn S. Toward a synthetic hydrogen sensor in cyanobacteria: Functional production of an oxygen-tolerant regulatory hydrogenase in Synechocystis sp. PCC 6803. Front Microbiol 2023; 14:1122078. [PMID: 37032909 PMCID: PMC10073562 DOI: 10.3389/fmicb.2023.1122078] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 02/22/2023] [Indexed: 04/11/2023] Open
Abstract
Cyanobacteria have raised great interest in biotechnology, e.g., for the sustainable production of molecular hydrogen (H2) using electrons from water oxidation. However, this is hampered by various constraints. For example, H2-producing enzymes compete with primary metabolism for electrons and are usually inhibited by molecular oxygen (O2). In addition, there are a number of other constraints, some of which are unknown, requiring unbiased screening and systematic engineering approaches to improve the H2 yield. Here, we introduced the regulatory [NiFe]-hydrogenase (RH) of Cupriavidus necator (formerly Ralstonia eutropha) H16 into the cyanobacterial model strain Synechocystis sp. PCC 6803. In its natural host, the RH serves as a molecular H2 sensor initiating a signal cascade to express hydrogenase-related genes when no additional energy source other than H2 is available. Unlike most hydrogenases, the C. necator enzymes are O2-tolerant, allowing their efficient utilization in an oxygenic phototroph. Similar to C. necator, the RH produced in Synechocystis showed distinct H2 oxidation activity, confirming that it can be properly matured and assembled under photoautotrophic, i.e., oxygen-evolving conditions. Although the functional H2-sensing cascade has not yet been established in Synechocystis yet, we utilized the associated two-component system consisting of a histidine kinase and a response regulator to drive and modulate the expression of a superfolder gfp gene in Escherichia coli. This demonstrates that all components of the H2-dependent signal cascade can be functionally implemented in heterologous hosts. Thus, this work provides the basis for the development of an intrinsic H2 biosensor within a cyanobacterial cell that could be used to probe the effects of random mutagenesis and systematically identify promising genetic configurations to enable continuous and high-yield production of H2 via oxygenic photosynthesis.
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Affiliation(s)
- Franz Opel
- Department of Solar Materials, Helmholtz Centre for Environmental Research – UFZ, Leipzig, Germany
| | | | - Isabel Wehner
- Department of Solar Materials, Helmholtz Centre for Environmental Research – UFZ, Leipzig, Germany
| | - Sara Lupacchini
- Department of Solar Materials, Helmholtz Centre for Environmental Research – UFZ, Leipzig, Germany
| | - Lars Lauterbach
- Institute of Applied Microbiology (iAMB), RWTH Aachen University, Aachen, Germany
| | - Oliver Lenz
- Institute of Chemistry, Technical University of Berlin, Berlin, Germany
| | - Stephan Klähn
- Department of Solar Materials, Helmholtz Centre for Environmental Research – UFZ, Leipzig, Germany
- *Correspondence: Stephan Klähn,
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Fan Q, Caserta G, Lorent C, Zebger I, Neubauer P, Lenz O, Gimpel M. High-Yield Production of Catalytically Active Regulatory [NiFe]-Hydrogenase From Cupriavidus necator in Escherichia coli. Front Microbiol 2022; 13:894375. [PMID: 35572669 PMCID: PMC9100943 DOI: 10.3389/fmicb.2022.894375] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 04/08/2022] [Indexed: 11/13/2022] Open
Abstract
Hydrogenases are biotechnologically relevant metalloenzymes that catalyze the reversible conversion of molecular hydrogen into protons and electrons. The O2-tolerant [NiFe]-hydrogenases from Cupriavidus necator (formerly Ralstonia eutropha) are of particular interest as they maintain catalysis even in the presence of molecular oxygen. However, to meet the demands of biotechnological applications and scientific research, a heterologous production strategy is required to overcome the low production yields in their native host. We have previously used the regulatory hydrogenase (RH) from C. necator as a model for the development of such a heterologous hydrogenase production process in E. coli. Although high protein yields were obtained, the purified enzyme was inactive due to the lack of the catalytic center, which contains an inorganic nickel-iron cofactor. In the present study, we significantly improved the production process to obtain catalytically active RH. We optimized important factors such as O2 content, metal availability, production temperature and time as well as the co-expression of RH-specific maturase genes. The RH was successfully matured during aerobic cultivation of E. coli by co-production of seven hydrogenase-specific maturases and a nickel permease, which was confirmed by activity measurements and spectroscopic investigations of the purified enzyme. The improved production conditions resulted in a high yield of about 80 mg L–1 of catalytically active RH and an up to 160-fold space-time yield in E. coli compared to that in the native host C. necator [<0.1 U (L d) –1]. Our strategy has important implications for the use of E. coli K-12 and B strains in the recombinant production of complex metalloenzymes, and provides a blueprint for the production of catalytically active [NiFe]-hydrogenases in biotechnologically relevant quantities.
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Affiliation(s)
- Qin Fan
- Chair of Bioprocess Engineering, Department of Biotechnology, Technische Universität Berlin, Berlin, Germany
| | - Giorgio Caserta
- Department of Chemistry, Technische Universität Berlin, Berlin, Germany
| | - Christian Lorent
- Department of Chemistry, Technische Universität Berlin, Berlin, Germany
| | - Ingo Zebger
- Department of Chemistry, Technische Universität Berlin, Berlin, Germany
| | - Peter Neubauer
- Chair of Bioprocess Engineering, Department of Biotechnology, Technische Universität Berlin, Berlin, Germany
| | - Oliver Lenz
- Department of Chemistry, Technische Universität Berlin, Berlin, Germany
| | - Matthias Gimpel
- Chair of Bioprocess Engineering, Department of Biotechnology, Technische Universität Berlin, Berlin, Germany
- *Correspondence: Matthias Gimpel,
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Fan Q, Caserta G, Lorent C, Lenz O, Neubauer P, Gimpel M. Optimization of Culture Conditions for Oxygen-Tolerant Regulatory [NiFe]-Hydrogenase Production from Ralstonia eutropha H16 in Escherichia coli. Microorganisms 2021; 9:1195. [PMID: 34073092 PMCID: PMC8229454 DOI: 10.3390/microorganisms9061195] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 05/21/2021] [Accepted: 05/28/2021] [Indexed: 11/16/2022] Open
Abstract
Hydrogenases are abundant metalloenzymes that catalyze the reversible conversion of molecular H2 into protons and electrons. Important achievements have been made over the past two decades in the understanding of these highly complex enzymes. However, most hydrogenases have low production yields requiring many efforts and high costs for cultivation limiting their investigation. Heterologous production of these hydrogenases in a robust and genetically tractable expression host is an attractive strategy to make these enzymes more accessible. In the present study, we chose the oxygen-tolerant H2-sensing regulatory [NiFe]-hydrogenase (RH) from Ralstonia eutropha H16 owing to its relatively simple architecture compared to other [NiFe]-hydrogenases as a model to develop a heterologous hydrogenase production system in Escherichia coli. Using screening experiments in 24 deep-well plates with 3 mL working volume, we investigated relevant cultivation parameters, including inducer concentration, expression temperature, and expression time. The RH yield could be increased from 14 mg/L up to >250 mg/L by switching from a batch to an EnPresso B-based fed-batch like cultivation in shake flasks. This yield exceeds the amount of RH purified from the homologous host R. eutropha by several 100-fold. Additionally, we report the successful overproduction of the RH single subunits HoxB and HoxC, suitable for biochemical and spectroscopic investigations. Even though both RH and HoxC proteins were isolated in an inactive, cofactor free apo-form, the proposed strategy may powerfully accelerate bioprocess development and structural studies for both basic research and applied studies. These results are discussed in the context of the regulation mechanisms governing the assembly of large and small hydrogenase subunits.
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Affiliation(s)
- Qin Fan
- Institute of Biotechnology, Technische Universität Berlin, Chair of Bioprocess Engineering, Ackerstraße 76, D-13355 Berlin, Germany; (Q.F.); (P.N.)
| | - Giorgio Caserta
- Department of Chemistry, Technische Universität Berlin, Straße des 17. Juni 135, D-10623 Berlin, Germany; (G.C.); (C.L.); (O.L.)
| | - Christian Lorent
- Department of Chemistry, Technische Universität Berlin, Straße des 17. Juni 135, D-10623 Berlin, Germany; (G.C.); (C.L.); (O.L.)
| | - Oliver Lenz
- Department of Chemistry, Technische Universität Berlin, Straße des 17. Juni 135, D-10623 Berlin, Germany; (G.C.); (C.L.); (O.L.)
| | - Peter Neubauer
- Institute of Biotechnology, Technische Universität Berlin, Chair of Bioprocess Engineering, Ackerstraße 76, D-13355 Berlin, Germany; (Q.F.); (P.N.)
| | - Matthias Gimpel
- Institute of Biotechnology, Technische Universität Berlin, Chair of Bioprocess Engineering, Ackerstraße 76, D-13355 Berlin, Germany; (Q.F.); (P.N.)
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Fan Q, Neubauer P, Lenz O, Gimpel M. Heterologous Hydrogenase Overproduction Systems for Biotechnology-An Overview. Int J Mol Sci 2020; 21:E5890. [PMID: 32824336 PMCID: PMC7460606 DOI: 10.3390/ijms21165890] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 08/06/2020] [Accepted: 08/14/2020] [Indexed: 01/16/2023] Open
Abstract
Hydrogenases are complex metalloenzymes, showing tremendous potential as H2-converting redox catalysts for application in light-driven H2 production, enzymatic fuel cells and H2-driven cofactor regeneration. They catalyze the reversible oxidation of hydrogen into protons and electrons. The apo-enzymes are not active unless they are modified by a complicated post-translational maturation process that is responsible for the assembly and incorporation of the complex metal center. The catalytic center is usually easily inactivated by oxidation, and the separation and purification of the active protein is challenging. The understanding of the catalytic mechanisms progresses slowly, since the purification of the enzymes from their native hosts is often difficult, and in some case impossible. Over the past decades, only a limited number of studies report the homologous or heterologous production of high yields of hydrogenase. In this review, we emphasize recent discoveries that have greatly improved our understanding of microbial hydrogenases. We compare various heterologous hydrogenase production systems as well as in vitro hydrogenase maturation systems and discuss their perspectives for enhanced biohydrogen production. Additionally, activities of hydrogenases isolated from either recombinant organisms or in vivo/in vitro maturation approaches were systematically compared, and future perspectives for this research area are discussed.
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Affiliation(s)
- Qin Fan
- Institute of Biotechnology, Technical University of Berlin, Ackerstraße 76, 13355 Berlin, Germany; (Q.F.); (P.N.)
| | - Peter Neubauer
- Institute of Biotechnology, Technical University of Berlin, Ackerstraße 76, 13355 Berlin, Germany; (Q.F.); (P.N.)
| | - Oliver Lenz
- Department of Chemistry, Technical University of Berlin, Straße des 17. Juni 135, 10623 Berlin, Germany;
| | - Matthias Gimpel
- Institute of Biotechnology, Technical University of Berlin, Ackerstraße 76, 13355 Berlin, Germany; (Q.F.); (P.N.)
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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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Abstract
[NiFe]-hydrogenases catalyze the reversible conversion of hydrogen gas into protons and electrons and are vital metabolic components of many species of bacteria and archaea. At the core of this enzyme is a sophisticated catalytic center comprising nickel and iron, as well as cyanide and carbon monoxide ligands, which is anchored to the large hydrogenase subunit through cysteine residues. The production of this multicomponent active site is accomplished by a collection of accessory proteins and can be divided into discrete stages. The iron component is fashioned by the proteins HypC, HypD, HypE, and HypF, which functionalize iron with cyanide and carbon monoxide. Insertion of the iron center signals to the metallochaperones HypA, HypB, and SlyD to selectively deliver the nickel to the active site. A specific protease recognizes the completed metal cluster and then cleaves the C-terminus of the large subunit, resulting in a conformational change that locks the active site in place. Finally, the large subunit associates with the small subunit, and the complete holoenzyme translocates to its final cellular position. Beyond this broad overview of the [NiFe]-hydrogenase maturation process, biochemical and structural studies are revealing the fundamental underlying molecular mechanisms. Here, we review recent work illuminating how the accessory proteins contribute to the maturation of [NiFe]-hydrogenase and discuss some of the outstanding questions that remain to be resolved.
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Affiliation(s)
- Michael J Lacasse
- Department of Chemistry, University of Toronto , Toronto, Ontario, Canada M5S 3H6
| | - Deborah B Zamble
- Department of Chemistry, University of Toronto , Toronto, Ontario, Canada M5S 3H6.,Department of Biochemistry, University of Toronto , Toronto, Ontario, Canada M5S 1A8
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[NiFe]-hydrogenase maturation in vitro: analysis of the roles of the HybG and HypD accessory proteins1. Biochem J 2015; 464:169-77. [PMID: 25184670 DOI: 10.1042/bj20140485] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
[NiFe]-hydrogenases (Hyd) bind a nickel-iron-based cofactor. The Fe ion of the cofactor is bound by two cyanide ligands and a single carbon monoxide ligand. Minimally six accessory proteins (HypA-HypF) are necessary for NiFe(CN)2CO cofactor biosynthesis in Escherichia coli. It has been shown that the anaerobically purified HypC-HypD-HypE scaffold complex carries the Fe(CN)2CO moiety of this cofactor. In the present study, we have purified the HybG-HypDE complex and used it to successfully reconstitute in vitro active Hyd from E. coli. HybG is a homologue of HypC that is specifically required for the maturation of Hyd-2 and also functions in the maturation of Hyd-1 of E. coli. Maturation of active Hyd-1 and Hyd-2 could be demonstrated in extracts derived from HybG- and HypD-deficient E. coli strains by adding anaerobically purified HybG-HypDE complex. In vitro maturation was dependent on ATP, carbamoylphosphate, nickel and reducing conditions. Hydrogenase maturation was prevented when the purified HybG-HypDE complex used in the maturation assay lacked a bound Fe(CN)2CO moiety. These findings demonstrate that it is possible to isolate incompletely processed intermediates on the maturation pathway and to use these to activate apo-forms of [NiFe]-hydrogenase large subunits.
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Stripp ST, Lindenstrauss U, Granich C, Sawers RG, Soboh B. The influence of oxygen on [NiFe]-hydrogenase cofactor biosynthesis and how ligation of carbon monoxide precedes cyanation. PLoS One 2014; 9:e107488. [PMID: 25211029 PMCID: PMC4161419 DOI: 10.1371/journal.pone.0107488] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Accepted: 08/13/2014] [Indexed: 01/14/2023] Open
Abstract
The class of [NiFe]–hydrogenases is characterized by a bimetallic cofactor comprising low–spin nickel and iron ions, the latter of which is modified with a single carbon monoxide (CO) and two cyanide (CN−) molecules. Generation of these ligands in vivo requires a complex maturation apparatus in which the HypC–HypD complex acts as a ‘construction site’ for the Fe–(CN)2CO portion of the cofactor. The order of addition of the CO and CN– ligands determines the ultimate structure and catalytic efficiency of the cofactor; however much debate surrounds the succession of events. Here, we present an FT–IR spectroscopic analysis of HypC–HypD isolated from a hydrogenase–competent wild–type strain of Escherichia coli. In contrast to previously reported samples, HypC–HypD showed spectral contributions indicative of an electron–rich Fe–CO cofactor, at the same time lacking any Fe–CN– signatures. This immature iron site binds external CO and undergoes oxidative damage when in contact with O2. Binding of CO protects the site against loss of spectral features associated with O2 damage. Our findings strongly suggest that CO ligation precedes cyanation in vivo. Furthermore, the results provide a rationale for the deleterious effects of O2 on in vivo cofactor biosynthesis.
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Affiliation(s)
- Sven T Stripp
- Department of Physics, Freie Universität Berlin, Berlin, Germany
| | - Ute Lindenstrauss
- Institute of Microbiology, Martin-Luther Universität Halle-Wittenberg, Halle (Saale), Germany
| | - Claudia Granich
- Institute of Microbiology, Martin-Luther Universität Halle-Wittenberg, Halle (Saale), Germany
| | - R Gary Sawers
- Institute of Microbiology, Martin-Luther Universität Halle-Wittenberg, Halle (Saale), Germany
| | - Basem Soboh
- Institute of Microbiology, Martin-Luther Universität Halle-Wittenberg, Halle (Saale), Germany
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Shepard EM, Mus F, Betz JN, Byer AS, Duffus BR, Peters JW, Broderick JB. [FeFe]-hydrogenase maturation. Biochemistry 2014; 53:4090-104. [PMID: 24878200 DOI: 10.1021/bi500210x] [Citation(s) in RCA: 87] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Hydrogenases are metalloenzymes that catalyze the reversible reduction of protons at unusual metal centers. This Current Topic discusses recent advances in elucidating the steps involved in the biosynthesis of the complex metal cluster at the [FeFe]-hydrogenase (HydA) active site, known as the H-cluster. The H-cluster is composed of a 2Fe subcluster that is anchored within the active site by a bridging cysteine thiolate to a [4Fe-4S] cubane. The 2Fe subcluster contains carbon monoxide, cyanide, and bridging dithiolate ligands. H-cluster biosynthesis is now understood to occur stepwise; standard iron-sulfur cluster assembly machinery builds the [4Fe-4S] cubane of the H-cluster, while three specific maturase enzymes known as HydE, HydF, and HydG assemble the 2Fe subcluster. HydE and HydG are both radical S-adenosylmethionine enzymes that interact with an iron-sulfur cluster binding GTPase scaffold, HydF, during the construction of the 2Fe subcluster moiety. In an unprecedented biochemical reaction, HydG cleaves tyrosine and decomposes the resulting dehydroglycine into carbon monoxide and cyanide ligands. The role of HydE in the biosynthetic pathway remains undefined, although it is hypothesized to be critical for the synthesis of the bridging dithiolate. HydF is the site where the complete 2Fe subcluster is formed and ultimately delivered to the immature hydrogenase protein in the final step of [FeFe]-hydrogenase maturation. This work addresses the roles of and interactions among HydE, HydF, HydG, and HydA in the formation of the mature [FeFe]-hydrogenase.
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Affiliation(s)
- Eric M Shepard
- Department of Chemistry and Biochemistry, Montana State University , Bozeman, Montana 59717, United States
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Affiliation(s)
- Wolfgang Lubitz
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Hideaki Ogata
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Olaf Rüdiger
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Edward Reijerse
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, 45470 Mülheim an der Ruhr, Germany
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11
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Soboh B, Stripp ST, Bielak C, Lindenstrauß U, Braussemann M, Javaid M, Hallensleben M, Granich C, Herzberg M, Heberle J, Sawers RG. The [NiFe]-hydrogenase accessory chaperones HypC and HybG of Escherichia coli are iron- and carbon dioxide-binding proteins. FEBS Lett 2013; 587:2512-6. [PMID: 23851071 DOI: 10.1016/j.febslet.2013.06.055] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2013] [Revised: 06/27/2013] [Accepted: 06/27/2013] [Indexed: 12/26/2022]
Abstract
[NiFe]-hydrogenase accessory proteins HypC and HypD form a complex that binds a Fe-(CN)₂CO moiety and CO₂. In this study two HypC homologues from Escherichia coli were purified under strictly anaerobic conditions and both contained sub-stoichiometric amounts of iron (approx. 0.3 molFe/mol HypC). Infrared spectroscopic analysis identified a signature at 2337 cm⁻¹ indicating bound CO₂. Aerobically isolated HypC lacked both Fe and CO₂. Exchange of either of the highly conserved amino acid residues Cys2 or His51 abolished both Fe- and CO₂-binding. Our results suggest that HypC delivers CO₂ bound directly to Fe for reduction to CO by HypD.
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Affiliation(s)
- Basem Soboh
- Institute of Microbiology, Martin-Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3, 06120 Halle (Saale), Germany
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12
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Schiffels J, Pinkenburg O, Schelden M, Aboulnaga EHAA, Baumann MEM, Selmer T. An innovative cloning platform enables large-scale production and maturation of an oxygen-tolerant [NiFe]-hydrogenase from Cupriavidus necator in Escherichia coli. PLoS One 2013; 8:e68812. [PMID: 23861944 PMCID: PMC3702609 DOI: 10.1371/journal.pone.0068812] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2013] [Accepted: 05/31/2013] [Indexed: 11/18/2022] Open
Abstract
Expression of multiple heterologous genes in a dedicated host is a prerequisite for approaches in synthetic biology, spanning from the production of recombinant multiprotein complexes to the transfer of tailor-made metabolic pathways. Such attempts are often exacerbated, due in most cases to a lack of proper directional, robust and readily accessible genetic tools. Here, we introduce an innovative system for cloning and expression of multiple genes in Escherichia coli BL21 (DE3). Using the novel methodology, genes are equipped with individual promoters and terminators and subsequently assembled. The resulting multiple gene cassettes may either be placed in one vector or alternatively distributed among a set of compatible plasmids. We demonstrate the effectiveness of the developed tool by production and maturation of the NAD(+)reducing soluble [NiFe]-hydrogenase (SH) from Cupriavidus necator H16 (formerly Ralstonia eutropha H16) in E. coli BL21Star™ (DE3). The SH (encoded in hoxFUYHI) was successfully matured by co-expression of a dedicated set of auxiliary genes, comprising seven hyp genes (hypC1D1E1A2B2F2X) along with hoxW, which encodes a specific endopeptidase. Deletion of genes involved in SH maturation reduced maturation efficiency substantially. Further addition of hoxN1, encoding a high-affinity nickel permease from C. necator, considerably increased maturation efficiency in E. coli. Carefully balanced growth conditions enabled hydrogenase production at high cell-densities, scoring mg·(Liter culture)(-1) yields of purified functional SH. Specific activities of up to 7.2±1.15 U·mg(-1) were obtained in cell-free extracts, which is in the range of the highest activities ever determined in C. necator extracts. The recombinant enzyme was isolated in equal purity and stability as previously achieved with the native form, yielding ultrapure preparations with anaerobic specific activities of up to 230 U·mg(-1). Owing to the combinatorial power exhibited by the presented cloning platform, the system might represent an important step towards new routes in synthetic biology.
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Affiliation(s)
- Johannes Schiffels
- Department of Chemistry and Biotechnology, Aachen University of Applied Sciences, Juelich, Germany
| | - Olaf Pinkenburg
- Institute for Immunology, Biomedical Research Centre (BMFZ), Philipps University of Marburg, Marburg (Lahn), Germany
| | - Maximilian Schelden
- Department of Chemistry and Biotechnology, Aachen University of Applied Sciences, Juelich, Germany
| | | | - Marcus E. M. Baumann
- Department of Chemistry and Biotechnology, Aachen University of Applied Sciences, Juelich, Germany
| | - Thorsten Selmer
- Department of Chemistry and Biotechnology, Aachen University of Applied Sciences, Juelich, Germany
- * E-mail:
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13
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Albareda M, Manyani H, Imperial J, Brito B, Ruiz-Argüeso T, Böck A, Palacios JM. Dual role of HupF in the biosynthesis of [NiFe] hydrogenase in Rhizobium leguminosarum. BMC Microbiol 2012; 12:256. [PMID: 23136881 PMCID: PMC3534401 DOI: 10.1186/1471-2180-12-256] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2012] [Accepted: 10/24/2012] [Indexed: 11/16/2022] Open
Abstract
Background [NiFe] hydrogenases are enzymes that catalyze the oxidation of hydrogen into protons and electrons, to use H2 as energy source, or the production of hydrogen through proton reduction, as an escape valve for the excess of reduction equivalents in anaerobic metabolism. Biosynthesis of [NiFe] hydrogenases is a complex process that occurs in the cytoplasm, where a number of auxiliary proteins are required to synthesize and insert the metal cofactors into the enzyme structural units. The endosymbiotic bacterium Rhizobium leguminosarum requires the products of eighteen genes (hupSLCDEFGHIJKhypABFCDEX) to synthesize an active hydrogenase. hupF and hupK genes are found only in hydrogenase clusters from bacteria expressing hydrogenase in the presence of oxygen. Results HupF is a HypC paralogue with a similar predicted structure, except for the C-terminal domain present only in HupF. Deletion of hupF results in the inability to process the hydrogenase large subunit HupL, and also in reduced stability of this subunit when cells are exposed to high oxygen tensions. A ΔhupF mutant was fully complemented for hydrogenase activity by a C-terminal deletion derivative under symbiotic, ultra low-oxygen tensions, but only partial complementation was observed in free living cells under higher oxygen tensions (1% or 3%). Co-purification experiments using StrepTag-labelled HupF derivatives and mass spectrometry analysis indicate the existence of a major complex involving HupL and HupF, and a less abundant HupF-HupK complex. Conclusions The results indicate that HupF has a dual role during hydrogenase biosynthesis: it is required for hydrogenase large subunit processing and it also acts as a chaperone to stabilize HupL when hydrogenase is synthesized in the presence of oxygen.
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Affiliation(s)
- Marta Albareda
- Centro de Biotecnología y Genómica de Plantas-CBGP, Universidad Politécnica de Madrid, Campus de Montegancedo, Carretera M40- km 37.7, 28223 Pozuelo de Alarcón, Madrid, Spain
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Bürstel I, Siebert E, Winter G, Hummel P, Zebger I, Friedrich B, Lenz O. A universal scaffold for synthesis of the Fe(CN)2(CO) moiety of [NiFe] hydrogenase. J Biol Chem 2012; 287:38845-53. [PMID: 23019332 DOI: 10.1074/jbc.m112.376947] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Hydrogen-cycling [NiFe] hydrogenases harbor a dinuclear catalytic center composed of nickel and iron ions, which are coordinated by four cysteine residues. Three unusual diatomic ligands in the form of two cyanides (CN(-)) and one carbon monoxide (CO) are bound to the iron and apparently account for the complexity of the cofactor assembly process, which involves the function of at least six auxiliary proteins, designated HypA, -B, -C, -D, -E, and -F. It has been demonstrated previously that the HypC, -D, -E, and -F proteins participate in cyanide synthesis and transfer. Here, we show by infrared spectroscopic analysis that the purified HypCD complexes from Ralstonia eutropha and Escherichia coli carry in addition to both cyanides the CO ligand. We present experimental evidence that in vivo the attachment of the CN(-) ligands is a prerequisite for subsequent CO binding. With the aid of genetic engineering and subsequent mutant analysis, the functional role of conserved cysteine residues in HypD from R. eutropha was investigated. Our results demonstrate that the HypCD complex serves as a scaffold for the assembly of the Fe(CN)(2)(CO) entity of [NiFe] hydrogenase.
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Affiliation(s)
- Ingmar Bürstel
- Institut für Biologie/Mikrobiologie, Humboldt-Universität zu Berlin, Chausseestrasse 117,10115 Berlin, Germany
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15
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Soboh B, Stripp ST, Muhr E, Granich C, Braussemann M, Herzberg M, Heberle J, Gary Sawers R. [NiFe]-hydrogenase maturation: Isolation of a HypC-HypD complex carrying diatomic CO and CN−
ligands. FEBS Lett 2012; 586:3882-7. [DOI: 10.1016/j.febslet.2012.09.019] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2012] [Revised: 09/12/2012] [Accepted: 09/13/2012] [Indexed: 10/27/2022]
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16
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Shomura Y, Higuchi Y. Structural basis for the reaction mechanism of S-carbamoylation of HypE by HypF in the maturation of [NiFe]-hydrogenases. J Biol Chem 2012; 287:28409-19. [PMID: 22740694 DOI: 10.1074/jbc.m112.387134] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
As a remarkable structural feature of hydrogenase active sites, [NiFe]-hydrogenases harbor one carbonyl and two cyano ligands, where HypE and HypF are involved in the biosynthesis of the nitrile group as a precursor of the cyano groups. HypF catalyzes S-carbamoylation of the C-terminal cysteine of HypE via three steps using carbamoylphosphate and ATP, producing two unstable intermediates: carbamate and carbamoyladenylate. Although the crystal structures of intact HypE homodimers and partial HypF have been reported, it remains unclear how the consecutive reactions occur without the loss of unstable intermediates during the proposed reaction scheme. Here we report the crystal structures of full-length HypF both alone and in complex with HypE at resolutions of 2.0 and 2.6 Å, respectively. Three catalytic sites of the structures of the HypF nucleotide- and phosphate-bound forms have been identified, with each site connected via channels inside the protein. This finding suggests that the first two consecutive reactions occur without the release of carbamate or carbamoyladenylate from the enzyme. The structure of HypF in complex with HypE revealed that HypF can associate with HypE without disturbing its homodimeric interaction and that the binding manner allows the C-terminal Cys-351 of HypE to access the S-carbamoylation active site in HypF, suggesting that the third step can also proceed without the release of carbamoyladenylate. A comparison of the structure of HypF with the recently reported structures of O-carbamoyltransferase revealed different reaction mechanisms for carbamoyladenylate synthesis and a similar reaction mechanism for carbamoyltransfer to produce the carbamoyl-HypE molecule.
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Affiliation(s)
- Yasuhito Shomura
- Department of Life Science, Graduate School of Life Science, University of Hyogo, Hyogo 678-1297, Japan.
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17
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Chan KH, Lee KM, Wong KB. Interaction between hydrogenase maturation factors HypA and HypB is required for [NiFe]-hydrogenase maturation. PLoS One 2012; 7:e32592. [PMID: 22384275 PMCID: PMC3287977 DOI: 10.1371/journal.pone.0032592] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2011] [Accepted: 01/27/2012] [Indexed: 12/25/2022] Open
Abstract
The active site of [NiFe]-hydrogenase contains nickel and iron coordinated by cysteine residues, cyanide and carbon monoxide. Metal chaperone proteins HypA and HypB are required for the nickel insertion step of [NiFe]-hydrogenase maturation. How HypA and HypB work together to deliver nickel to the catalytic core remains elusive. Here we demonstrated that HypA and HypB from Archaeoglobus fulgidus form 1:1 heterodimer in solution and HypA does not interact with HypB dimer preloaded with GMPPNP and Ni. Based on the crystal structure of A. fulgidus HypB, mutants were designed to map the HypA binding site on HypB. Our results showed that two conserved residues, Tyr-4 and Leu-6, of A. fulgidus HypB are required for the interaction with HypA. Consistent with this observation, we demonstrated that the corresponding residues, Leu-78 and Val-80, located at the N-terminus of the GTPase domain of Escherichia coli HypB were required for HypA/HypB interaction. We further showed that L78A and V80A mutants of HypB failed to reactivate hydrogenase in an E. coli ΔhypB strain. Our results suggest that the formation of the HypA/HypB complex is essential to the maturation process of hydrogenase. The HypA binding site is in proximity to the metal binding site of HypB, suggesting that the HypA/HypB interaction may facilitate nickel transfer between the two proteins.
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Affiliation(s)
| | | | - Kam-Bo Wong
- School of Life Sciences, Centre for Protein Science and Crystallography, The Chinese University of Hong Kong, Shatin, Hong Kong Special Administrative Region, People's Republic of China
- * E-mail:
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18
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Structural basis for GTP-dependent dimerization of hydrogenase maturation factor HypB. PLoS One 2012; 7:e30547. [PMID: 22276211 PMCID: PMC3262836 DOI: 10.1371/journal.pone.0030547] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2011] [Accepted: 12/19/2011] [Indexed: 12/13/2022] Open
Abstract
Maturation of [NiFe]-hydrogenase requires the insertion of iron, cyanide and carbon monoxide, followed by nickel, to the catalytic core of the enzyme. Hydrogenase maturation factor HypB is a metal-binding GTPase that is essential for the nickel delivery to the hydrogenase. Here we report the crystal structure of Archeoglobus fulgidus HypB (AfHypB) in apo-form. We showed that AfHypB recognizes guanine nucleotide using Asp-194 on the G5 loop despite having a non-canonical NKxA G4-motif. Structural comparison with the GTPγS-bound Methanocaldococcus jannaschii HypB identifies conformational changes in the switch I region, which bring an invariant Asp-72 to form an intermolecular salt-bridge with another invariant residue Lys-148 upon GTP binding. Substitution of K148A abolished GTP-dependent dimerization of AfHypB, but had no significant effect on the guanine nucleotide binding and on the intrinsic GTPase activity. In vivo complementation study in Escherichia coli showed that the invariant lysine residue is required for in vivo maturation of hydrogenase. Taken together, our results suggest that GTP-dependent dimerization of HypB is essential for hydrogenase maturation. It is likely that a nickel ion is loaded to an extra metal binding site at the dimeric interface of GTP-bound HypB and transferred to the hydrogenase upon GTP hydrolysis.
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Bürstel I, Hummel P, Siebert E, Wisitruangsakul N, Zebger I, Friedrich B, Lenz O. Probing the origin of the metabolic precursor of the CO ligand in the catalytic center of [NiFe] hydrogenase. J Biol Chem 2011; 286:44937-44. [PMID: 22049085 DOI: 10.1074/jbc.m111.309351] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The O(2)-tolerant [NiFe] hydrogenases of Ralstonia eutropha are capable of H(2) conversion in the presence of ambient O(2). Oxygen represents not only a challenge for catalysis but also for the complex assembling process of the [NiFe] active site. Apart from nickel and iron, the catalytic center contains unusual diatomic ligands, namely two cyanides (CN(-)) and one carbon monoxide (CO), which are coordinated to the iron. One of the open questions of the maturation process concerns the origin and biosynthesis of the CO group. Isotope labeling in combination with infrared spectroscopy revealed that externally supplied gaseous (13)CO serves as precursor of the carbonyl group of the regulatory [NiFe] hydrogenase in R. eutropha. Corresponding (13)CO titration experiments showed that a concentration 130-fold higher than ambient CO (0.1 ppmv) caused a 50% labeling of the carbonyl ligand in the [NiFe] hydrogenase, leading to the conclusion that the carbonyl ligand originates from an intracellular metabolite. A novel setup allowed us to the study effects of CO depletion on maturation in vivo. Upon induction of CO depletion by addition of the CO scavenger PdCl(2), cells cultivated on H(2), CO(2), and O(2) showed severe growth retardation at low cell concentrations, which was on the basis of partially arrested hydrogenase maturation, leading to reduced hydrogenase activity. This suggests gaseous CO as a metabolic precursor under these conditions. The addition of PdCl(2) to cells cultivated heterotrophically on organic substrates had no effect on hydrogenase maturation. These results indicate at least two different pathways for biosynthesis of the CO ligand of [NiFe] hydrogenase.
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Affiliation(s)
- Ingmar Bürstel
- Humboldt-Universität zu Berlin, Institut für Biologie/Mikrobiologie, Chausseestrasse 117, 10115 Berlin, Germany
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20
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Pinske C, Bönn M, Krüger S, Lindenstrauß U, Sawers RG. Metabolic deficiences revealed in the biotechnologically important model bacterium Escherichia coli BL21(DE3). PLoS One 2011; 6:e22830. [PMID: 21826210 PMCID: PMC3149613 DOI: 10.1371/journal.pone.0022830] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2011] [Accepted: 07/01/2011] [Indexed: 11/26/2022] Open
Abstract
The Escherichia coli B strain BL21(DE3) has had a profound impact on biotechnology through its use in the production of recombinant proteins. Little is understood, however, regarding the physiology of this important E. coli strain. We show here that BL21(DE3) totally lacks activity of the four [NiFe]-hydrogenases, the three molybdenum- and selenium-containing formate dehydrogenases and molybdenum-dependent nitrate reductase. Nevertheless, all of the structural genes necessary for the synthesis of the respective anaerobic metalloenzymes are present in the genome. However, the genes encoding the high-affinity molybdate transport system and the molybdenum-responsive transcriptional regulator ModE are absent from the genome. Moreover, BL21(DE3) has a nonsense mutation in the gene encoding the global oxygen-responsive transcriptional regulator FNR. The activities of the two hydrogen-oxidizing hydrogenases, therefore, could be restored to BL21(DE3) by supplementing the growth medium with high concentrations of Ni²⁺ (Ni²⁺-transport is FNR-dependent) or by introducing a wild-type copy of the fnr gene. Only combined addition of plasmid-encoded fnr and high concentrations of MoO₄²⁻ ions could restore hydrogen production to BL21(DE3); however, to only 25-30% of a K-12 wildtype. We could show that limited hydrogen production from the enzyme complex responsible for formate-dependent hydrogen evolution was due solely to reduced activity of the formate dehydrogenase (FDH-H), not the hydrogenase component. The activity of the FNR-dependent formate dehydrogenase, FDH-N, could not be restored, even when the fnr gene and MoO₄²⁻ were supplied; however, nitrate reductase activity could be recovered by combined addition of MoO₄²⁻ and the fnr gene. This suggested that a further component specific for biosynthesis or activity of formate dehydrogenases H and N was missing. Re-introduction of the gene encoding ModE could only partially restore the activities of both enzymes. Taken together these results demonstrate that BL21(DE3) has major defects in anaerobic metabolism, metal ion transport and metalloprotein biosynthesis.
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Affiliation(s)
- Constanze Pinske
- Institute for Microbiology, Martin-Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Markus Bönn
- Institute of Computer Science, Martin-Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Sara Krüger
- Institute for Microbiology, Martin-Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Ute Lindenstrauß
- Institute for Microbiology, Martin-Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - R. Gary Sawers
- Institute for Microbiology, Martin-Luther University Halle-Wittenberg, Halle (Saale), Germany
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21
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Swanson KD, Duffus BR, Beard TE, Peters JW, Broderick JB. Cyanide and Carbon Monoxide Ligand Formation in Hydrogenase Biosynthesis. Eur J Inorg Chem 2011. [DOI: 10.1002/ejic.201001056] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Kevin D. Swanson
- Department of Chemistry & Biochemistry, AstrobiologyBiogeocatalysis Research Center, Montana State University Bozeman, MT 59717, USA, Fax: +1‐406‐994‐7470
| | - Benjamin R. Duffus
- Department of Chemistry & Biochemistry, AstrobiologyBiogeocatalysis Research Center, Montana State University Bozeman, MT 59717, USA, Fax: +1‐406‐994‐7470
| | - Trevor E. Beard
- Department of Chemistry & Biochemistry, AstrobiologyBiogeocatalysis Research Center, Montana State University Bozeman, MT 59717, USA, Fax: +1‐406‐994‐7470
| | - John W. Peters
- Department of Chemistry & Biochemistry, AstrobiologyBiogeocatalysis Research Center, Montana State University Bozeman, MT 59717, USA, Fax: +1‐406‐994‐7470
| | - Joan B. Broderick
- Department of Chemistry & Biochemistry, AstrobiologyBiogeocatalysis Research Center, Montana State University Bozeman, MT 59717, USA, Fax: +1‐406‐994‐7470
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22
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Soboh B, Krüger S, Kuhns M, Pinske C, Lehmann A, Sawers RG. Development of a cell-free system reveals an oxygen-labile step in the maturation of [NiFe]-hydrogenase 2 ofEscherichia coli. FEBS Lett 2010; 584:4109-14. [DOI: 10.1016/j.febslet.2010.08.037] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2010] [Revised: 08/16/2010] [Accepted: 08/24/2010] [Indexed: 11/27/2022]
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23
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Pandelia ME, Ogata H, Lubitz W. Intermediates in the catalytic cycle of [NiFe] hydrogenase: functional spectroscopy of the active site. Chemphyschem 2010; 11:1127-40. [PMID: 20301175 DOI: 10.1002/cphc.200900950] [Citation(s) in RCA: 92] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The [NiFe] hydrogenase from the anaerobic sulphate reducing bacterium Desulfovibrio vulgaris Miyazaki F is an excellent model for constructing a mechanism for the function of the so-called 'oxygen-sensitive' hydrogenases. The present review focuses on spectroscopic investigations of the active site intermediates playing a role in the activation/deactivation and catalytic cycle of this enzyme as well as in the inhibition by carbon monoxide or molecular oxygen and the light-sensitivity of the hydrogenase. The methods employed include magnetic resonance and vibrational (FTIR) techniques combined with electrochemistry that deliver information about details of the geometrical and electronic structure of the intermediates and their redox behaviour. Based on these data a mechanistic scheme is developed.
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Affiliation(s)
- Maria-Eirini Pandelia
- Max-Planck Institut für Bioanorganische Chemie, Stiftstrasse 34-36, 45470, Mülheim an der Ruhr, Germany
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24
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Löscher S, Gebler A, Stein M, Sanganas O, Buhrke T, Zebger I, Dau H, Friedrich B, Lenz O, Haumann M. Protein-protein complex formation affects the Ni-Fe and Fe-S centers in the H2-sensing regulatory hydrogenase from Ralstonia eutropha H16. Chemphyschem 2010; 11:1297-306. [PMID: 20340124 DOI: 10.1002/cphc.200901007] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The regulatory Ni-Fe hydrogenase (RH) from the H(2)-oxidizing bacterium Ralstonia eutropha functions as an oxygen-resistant hydrogen sensor, which is composed of the large, active-site-containing HoxC subunit and the small subunit HoxB carrying Fe-S clusters. In vivo, the HoxBC subunits form a dimer designated as RH(wt). The RH(wt) protein transmits its signals to the histidine protein kinase HoxJ, which itself forms a homotetramer and a stable complex with RH(wt) (RH(wt)-HoxJ(wt)), located in the cytoplasm. In this study, we used X-ray absorption (XAS), electron paramagnetic resonance (EPR), and Fourier transform infrared (FTIR) spectroscopy to investigate the impact of various complexes between RH and HoxJ on the structural and electronic properties of the Ni-Fe active site and the Fe-S clusters. Aside from the RH(wt) protein and the RH(wt)-HoxJ(wt) complex, we investigated the RH(stop) protein, which consists of only one HoxB and HoxC unit due to the missing C-terminus of HoxB, as well as RH(wt)-HoxJ(Deltakinase), in which the histidine protein kinase lacks the transmitter domain. All constructs reacted with H(2), leading to the formation of the EPR-detectable Ni(III)-C state of the active site and to the reduction of Fe-S clusters detectable by XAS, thus corroborating that H(2) cleavage is independent of the presence of the HoxJ protein. In RH(stop), presumably one Fe-S cluster was lost during the preparation procedure. The coordination of the active site Ni in RH(stop) differed from that in RH(wt) and the RH(wt)-HoxJ complexes, in which additional Ni--O bonds were detected by XAS. The Ni--O bonds caused only very minor changes of the EPR g-values of the Ni-C and Ni-L states and of the IR vibrational frequencies of the diatomic CN(-) and CO ligands at the active-site Fe ion. Both one Fe-S cluster in HoxB and an oxygen-rich Ni coordination seem to be stabilized by RH dimerization involving the C-terminus of HoxB and by complex formation with HoxJ.
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Affiliation(s)
- Simone Löscher
- Experimental Physics, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
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Lenz O, Ludwig M, Schubert T, Bürstel I, Ganskow S, Goris T, Schwarze A, Friedrich B. H2 conversion in the presence of O2 as performed by the membrane-bound [NiFe]-hydrogenase of Ralstonia eutropha. Chemphyschem 2010; 11:1107-19. [PMID: 20186906 DOI: 10.1002/cphc.200901002] [Citation(s) in RCA: 89] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
[NiFe]-hydrogenases catalyze the oxidation of H(2) to protons and electrons. This reversible reaction is based on a complex interplay of metal cofactors including the Ni-Fe active site and several [Fe-S] clusters. H(2) catalysis of most [NiFe]-hydrogenases is sensitive to dioxygen. However, some bacteria contain hydrogenases that activate H(2) even in the presence of O(2). There is now compelling evidence that O(2) affects hydrogenase on three levels: 1) H(2) catalysis, 2) hydrogenase maturation, and 3) H(2)-mediated signal transduction. Herein, we summarize the genetic, biochemical, electrochemical, and spectroscopic properties related to the O(2) tolerance of hydrogenases resident in the facultative chemolithoautotroph Ralstonia eutropha H16. A focus is given to the membrane-bound [NiFe]-hydogenase, which currently represents the best-characterized member of O(2)-tolerant hydrogenases.
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Affiliation(s)
- Oliver Lenz
- Department of Microbiology, Humboldt-Universität zu Berlin, Chausseestrasse 117, 10115 Berlin, Germany.
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26
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Thauer RK, Kaster AK, Goenrich M, Schick M, Hiromoto T, Shima S. Hydrogenases from Methanogenic Archaea, Nickel, a Novel Cofactor, and H2Storage. Annu Rev Biochem 2010; 79:507-36. [DOI: 10.1146/annurev.biochem.030508.152103] [Citation(s) in RCA: 299] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
| | | | | | | | | | - Seigo Shima
- Max Planck Institute for Terrestrial Microbiology, D-35043 Marburg, Germany;
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27
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Affiliation(s)
- Thomas B Rauchfuss
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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28
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Rauchfuss T. Die Entschlüsselung der Biosynthese der schnellsten natürlichen Hydrogenase. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.201000597] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Winter G, Dökel S, Jones AK, Scheerer P, Krauss N, Höhne W, Friedrich B. Crystallization and preliminary X-ray crystallographic analysis of the [NiFe]-hydrogenase maturation factor HypF1 from Ralstonia eutropha H16. Acta Crystallogr Sect F Struct Biol Cryst Commun 2010; 66:452-5. [PMID: 20383020 PMCID: PMC2852342 DOI: 10.1107/s1744309110006196] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2009] [Accepted: 02/16/2010] [Indexed: 11/11/2022]
Abstract
The hydrogenase maturation factor HypF1 is a truncated but functional version of the HypF protein. HypF is known to be involved in the supply of the CN(-) ligands of the active site of [NiFe]-hydrogenases, utilizing carbamoyl phosphate as a substrate. The first crystallization and preliminary X-ray studies of HypF1 from Ralstonia eutropha H16 are reported here. Crystals of HypF1 (394 amino acids, 40.7 kDa) were obtained by the sitting-drop vapour-diffusion technique using sodium formate as a precipitant. The crystals belonged to space group I222, with unit-cell parameters a = 79.7, b = 91.6, c = 107.2 A. Complete X-ray diffraction data sets were collected at 100 K from native crystals and from a platinum derivative to a maximum resolution of 1.65 A.
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Affiliation(s)
- Gordon Winter
- Institut für Biologie/Mikrobiologie, Humboldt-Universität zu Berlin, Chausseestrasse 117, D-10115 Berlin, Germany
- Institut für Biochemie, Charité-Universitätsmedizin Berlin, Monbijoustrasse 2a, D-10117 Berlin, Germany
| | - Simon Dökel
- Institut für Biologie/Mikrobiologie, Humboldt-Universität zu Berlin, Chausseestrasse 117, D-10115 Berlin, Germany
- Institut für Biochemie, Charité-Universitätsmedizin Berlin, Monbijoustrasse 2a, D-10117 Berlin, Germany
| | - Anne K. Jones
- Institut für Biologie/Mikrobiologie, Humboldt-Universität zu Berlin, Chausseestrasse 117, D-10115 Berlin, Germany
| | - Patrick Scheerer
- Institut für Biochemie, Charité-Universitätsmedizin Berlin, Monbijoustrasse 2a, D-10117 Berlin, Germany
| | - Norbert Krauss
- Institut für Biochemie, Charité-Universitätsmedizin Berlin, Monbijoustrasse 2a, D-10117 Berlin, Germany
| | - Wolfgang Höhne
- Institut für Biochemie, Charité-Universitätsmedizin Berlin, Monbijoustrasse 2a, D-10117 Berlin, Germany
| | - Bärbel Friedrich
- Institut für Biologie/Mikrobiologie, Humboldt-Universität zu Berlin, Chausseestrasse 117, D-10115 Berlin, Germany
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30
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Crystal structure of HypA, a nickel-binding metallochaperone for [NiFe] hydrogenase maturation. J Mol Biol 2009; 394:448-59. [PMID: 19769985 DOI: 10.1016/j.jmb.2009.09.030] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2009] [Revised: 08/27/2009] [Accepted: 09/14/2009] [Indexed: 11/23/2022]
Abstract
HypA is one of the auxiliary proteins involved in the maturation of [NiFe] hydrogenases. By an unknown mechanism, HypA functions as a metallochaperone in the insertion of the Ni atom into hydrogenases. We have determined the crystal structures of HypA from Thermococcus kodakaraensis KOD1 in both monomeric and dimeric states. The structure of the HypA monomer consists of Ni- and Zn-binding domains. The relative arrangement of the two metal-binding domains has been shown to be associated with local conformations of the conserved Ni-binding motif, suggesting a communication between the Ni- and Zn-binding sites. The HypA dimer has been shown to be stabilized by unexpected domain swapping through archaea-specific linker helices. In addition, the hexameric structure of HypA is formed in the crystal packing. Several hydrogen bonds and hydrophobic interactions stabilize the hexamer interface. These findings suggest the functional diversity of HypA proteins.
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Affiliation(s)
- Yanjie Li
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON M5S 3H6, Canada
| | - Deborah B. Zamble
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON M5S 3H6, Canada
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32
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33
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McGlynn SE, Mulder DW, Shepard EM, Broderick JB, Peters JW. Hydrogenase cluster biosynthesis: organometallic chemistry nature's way. Dalton Trans 2009:4274-85. [PMID: 19662302 DOI: 10.1039/b821432h] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
It has been over a decade now since it was revealed that the metal containing active sites of hydrogenases possess carbonyl and cyanide ligands bound to iron. The presence of these ligands in hydrogenases came as a surprise and to-date these ligands have not been observed to be associated with any other enzymatic metallocenter. The elucidation of the structures of these unique metalloenzymes and their associated metal clusters created opportunity for a number of different lines of research. For synthetic chemists, the structures of hydrogenase active sites have provided attractive targets for syntheses that advance our understanding of the electronic structure and reactivity of these unique enzyme active sites. These efforts contribute to the synthesis of first row transition metal catalysts for hydrogen oxidation and hydrogen production that could have significant impacts on alternative and renewable energy solutions. Although effective synthetic approaches have been identified to generate models with a high degree of similarity to these active sites, the details of how these metal clusters are synthesized biochemically have not been resolved. Since hydrogen metabolism is presumed to be an early feature in the energetics of life and hydrogen metabolizing organisms can be traced very early in molecular phylogeny, the metal clusters at hydrogenase active sites are presumed to be among the earliest of known co-factors. Comparison of mineral based precursors and synthetic cluster analog chemistry to what is observed in contemporary biological systems may shed light on how proto-metabolically relevant catalysts first arose prebiotically by the processes of adoption of pre-existing functionality and ligand assisted catalysis.
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Affiliation(s)
- Shawn E McGlynn
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59715, USA
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Peters JW. Carbon Monoxide and Cyanide Ligands in the Active Site of [FeFe]-Hydrogenases. METAL-CARBON BONDS IN ENZYMES AND COFACTORS 2009. [DOI: 10.1039/9781847559333-00179] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The [FeFe]-hydrogenases, although share common features when compared to other metal containing hydrogenases, clearly have independent evolutionary origins. Examples of [FeFe]-hydrogenases have been characterized in detail by biochemical and spectroscopic approaches and the high resolution structures of two examples have been determined. The active site H-cluster is a complex bridged metal assembly in which a [4Fe-4S] cubane is bridged to a 2Fe subcluster with unique non-protein ligands including carbon monoxide, cyanide, and a five carbon dithiolate. Carbon monoxide and cyanide ligands as a component of a native active metal center is a property unique to the metal containing hydrogenases and there has been considerable attention to the characterization of the H-cluster at the level of electronic structure and mechanism as well as to defining the biological means to synthesize such a unique metal cluster. The chapter describes the structural architecture of [FeFe]-hydrogenases and key spectroscopic observations that have afforded the field with a fundamental basis for understanding the relationship between structure and reactivity of the H-cluster. In addition, the results and ideas concerning the topic of H-cluster biosynthesis as an emerging and fascinating area of research, effectively reinforcing the potential linkage between iron-sulfur biochemistry to the role of iron-sulfur minerals in prebiotic chemistry and the origin of life.
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Affiliation(s)
- John W. Peters
- Montana State University, Department of Chemistry and Biochemistry and the Astrobiology Biogeocatalysis Research Center Bozeman, MT 59717 USA
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English CM, Eckert C, Brown K, Seibert M, King PW. Recombinant and in vitro expression systems for hydrogenases: new frontiers in basic and applied studies for biological and synthetic H2 production. Dalton Trans 2009:9970-8. [DOI: 10.1039/b913426n] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Protein engineering of hydrogenase 3 to enhance hydrogen production. Appl Microbiol Biotechnol 2008; 79:77-86. [DOI: 10.1007/s00253-008-1416-3] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2008] [Revised: 02/07/2008] [Accepted: 02/12/2008] [Indexed: 01/12/2023]
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Nicolet Y, Rubach JK, Posewitz MC, Amara P, Mathevon C, Atta M, Fontecave M, Fontecilla-Camps JC. X-ray structure of the [FeFe]-hydrogenase maturase HydE from Thermotoga maritima. J Biol Chem 2008; 283:18861-72. [PMID: 18400755 DOI: 10.1074/jbc.m801161200] [Citation(s) in RCA: 97] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Maturation of the [FeFe]-hydrogenase active site depends on at least the expression of three gene products called HydE, HydF, and HydG. We have solved the high resolution structure of recombinant, reconstituted S-adenosine-L-methionine-dependent HydE from Thermotoga maritima. Besides the conserved [Fe(4)S(4)] cluster involved in the radical-based reaction, this HydE was reported to have a second [Fe(4)S(4)] cluster coordinated by three Cys residues. However, in our crystals, depending on the reconstitution and soaking conditions, this second cluster is either a [Fe(2)S(2)] center, with water occupying the fourth ligand site or is absent. We have carried out site-directed mutagenesis studies on the related HydE from Clostridium acetobutylicum, along with in silico docking and crystal soaking experiments, to define the active site region and three anion-binding sites inside a large, positive cavity, one of which binds SCN(-) with high affinity. Although the overall triose-phosphate isomerase-barrel structure of HydE is very similar to that of biotin synthase, the residues that line the internal cavity are significantly different in the two enzymes.
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Affiliation(s)
- Yvain Nicolet
- Laboratoire de Cristallographie et Cristallogenèse des Protéines, Institut de Biologie Structurale J.P. Ebel, Commissariat à l'Energie Atomique, CNRS, Université J. Fourier, 41 Rue J. Horowitz, 38027 Grenoble Cedex 1, France
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Structure of [NiFe] hydrogenase maturation protein HypE from Escherichia coli and its interaction with HypF. J Bacteriol 2007; 190:1447-58. [PMID: 18065529 DOI: 10.1128/jb.01610-07] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Hydrogenases are enzymes involved in hydrogen metabolism, utilizing H2 as an electron source. [NiFe] hydrogenases are heterodimeric Fe-S proteins, with a large subunit containing the reaction center involving Fe and Ni metal ions and a small subunit containing one or more Fe-S clusters. Maturation of the [NiFe] hydrogenase involves assembly of nonproteinaceous ligands on the large subunit by accessory proteins encoded by the hyp operon. HypE is an essential accessory protein and participates in the synthesis of two cyano groups found in the large subunit. We report the crystal structure of Escherichia coli HypE at 2.0-A resolution. HypE exhibits a fold similar to that of PurM and ThiL and forms dimers. The C-terminal catalytically essential Cys336 is internalized at the dimer interface between the N- and C-terminal domains. A mechanism for dehydration of the thiocarbamate to the thiocyanate is proposed, involving Asp83 and Glu272. The interactions of HypE and HypF were characterized in detail by surface plasmon resonance and isothermal titration calorimetry, revealing a Kd (dissociation constant) of approximately 400 nM. The stoichiometry and molecular weights of the complex were verified by size exclusion chromatography and gel scanning densitometry. These experiments reveal that HypE and HypF associate to form a stoichiometric, hetero-oligomeric complex predominantly consisting of a [EF]2 heterotetramer which exists in a dynamic equilibrium with the EF heterodimer. The surface plasmon resonance results indicate that a conformational change occurs upon heterodimerization which facilitates formation of a productive complex as part of the carbamate transfer reaction.
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