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Britt RD, Rauchfuss TB, Rao G. The H-cluster of [FeFe] Hydrogenases: Its Enzymatic Synthesis and Parallel Inorganic Semisynthesis. Acc Chem Res 2024; 57:1941-1950. [PMID: 38937148 PMCID: PMC11256358 DOI: 10.1021/acs.accounts.4c00231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Revised: 06/12/2024] [Accepted: 06/14/2024] [Indexed: 06/29/2024]
Abstract
ConspectusNature's prototypical hydrogen-forming catalysts─hydrogenases─have attracted much attention because they catalyze hydrogen evolution at near zero overpotential and ambient conditions. Beyond any possible applications in the energy sphere, the hydrogenases feature complicated active sites, which implies novel biosynthetic pathways. In terms of the variety of cofactors, the [FeFe]-hydrogenase is among the most complex.For more than a decade, we have worked on the biosynthesis of the active site of [FeFe] hydrogenases. This site, the H-cluster, is a six-iron ensemble consisting of a [4Fe-4S]H cluster linked to a [2Fe]H cluster that is coordinated to CO, cyanide, and a unique organic azadithiolate ligand. Many years ago, three enzymes, namely, HydG, HydE, and HydF, were shown to be required for the biosynthesis and the in vitro maturation of [FeFe] hydrogenases. The structures of the maturases were determined crystallographically, but still little progress was made on the biosynthetic pathway. As described in this Account, the elucidation of the biosynthetic pathway began in earnest with the identification of a molecular iron-cysteinate complex produced within HydG.In this Account, we present our most recent progress toward the molecular mechanism of [2Fe]H biosynthesis using a collaborative approach involving cell-free biosynthesis, isotope and element-sensitive spectroscopies, as well as inorganic synthesis of purported biosynthetic intermediates. Our study starts from the radical SAM enzyme HydG that lyses tyrosine into CO and cyanide and forms an Fe(CO)2(CN)-containing species. Crystallographic identification of a unique auxiliary 5Fe-4S cluster in HydG leads to a proposed catalytic cycle in which a free cysteine-chelated "dangler" Fe serves as the platform for the stepwise formation of a [4Fe-4S][Fe(CO)(CN)(cysteinate)] intermediate, which releases the [Fe(CO)2(CN)(cysteinate)] product, Complex B. Since Complex B is unstable, we applied synthetic organometallic chemistry to make an analogue, syn-B, and showed that it fully replaces HydG in the in vitro maturation of the H-cluster. Syn-B serves as the substrate for the next radical SAM enzyme HydE, where the low-spin Fe(II) center is activated by 5'-dAdo• to form an adenosylated Fe(I) intermediate. We propose that this Fe(I) species strips the carbon backbone and dimerizes in HydE to form a [Fe2(SH)2(CO)4(CN)2]2- product. This mechanistic scenario is supported by the use of a synthetic version of this dimer complex, syn-dimer, which allows for the formation of active hydrogenase with only the HydF maturase. Further application of this semisynthesis strategy shows that an [Fe2(SCH2NH2)2(CO)4(CN)2]2- complex can activate the apo hydrogenase, marking it as the last biosynthetic intermediate en route to the H-cluster. This combined enzymatic and semisynthetic approach greatly accelerates our understanding of H-cluster biosynthesis. We anticipate additional mechanistic details regarding H-cluster biosynthesis to be gleaned, and this methodology may be further applied in the study of other complex metallocofactors.
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Affiliation(s)
- R. David Britt
- Department
of Chemistry, University of California,
Davis, Davis, California 95616, United
States
| | - Thomas B. Rauchfuss
- Department
of Chemistry, University of Illinois at
Urbana−Champaign, Urbana, Illinois 61820, United States
| | - Guodong Rao
- Department
of Chemistry, University of California,
Davis, Davis, California 95616, United
States
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2
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Sun X, LaVoie M, Lefebvre PA, Gallaher SD, Glaesener AG, Strenkert D, Mehta R, Merchant SS, Silflow CD. Mutation of negative regulatory gene CEHC1 encoding an FBXO3 protein results in normoxic expression of HYDA genes in Chlamydomonas reinhardtii. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.22.586359. [PMID: 38586028 PMCID: PMC10996464 DOI: 10.1101/2024.03.22.586359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Oxygen is known to prevent hydrogen production in Chlamydomonas, both by inhibiting the hydrogenase enzyme and by preventing the accumulation of HYDA-encoding transcripts. We developed a screen for mutants showing constitutive accumulation of HYDA1 transcripts in the presence of oxygen. A reporter gene required for ciliary motility, placed under the control of the HYDA1 promoter, conferred motility only in hypoxic conditions. By selecting for mutants able to swim even in the presence of oxygen we obtained strains that express the reporter gene constitutively. One mutant identified a gene encoding an F-box only protein 3 (FBXO3), known to participate in ubiquitylation and proteasomal degradation pathways in other eukaryotes. Transcriptome profiles revealed that the mutation, termed cehc1-1 , leads to constitutive expression of HYDA1 and other genes regulated by hypoxia, and of many genes known to be targets of CRR1, a transcription factor in the nutritional copper signaling pathway. CRR1 was required for the constitutive expression of the HYDA1 reporter gene in cehc1-1 mutants. The CRR1 protein, which is normally degraded in Cu-supplemented cells, was stabilized in cehc1-1 cells, supporting the conclusion that CEHC1 acts to facilitate the degradation of CRR1. Our results reveal a novel negative regulator in the CRR1 pathway and possibly other pathways leading to complex metabolic changes associated with response to hypoxia.
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3
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Omeiri J, Martin L, Usclat A, Cherrier MV, Nicolet Y. Maturation of the [FeFe]-Hydrogenase: Direct Transfer of the (κ 3 -cysteinate)Fe II (CN)(CO) 2 Complex B from HydG to HydE. Angew Chem Int Ed Engl 2023; 62:e202314819. [PMID: 37962296 DOI: 10.1002/anie.202314819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Revised: 11/13/2023] [Accepted: 11/14/2023] [Indexed: 11/15/2023]
Abstract
[FeFe]-hydrogenases efficiently catalyze the reversible oxidation of molecular hydrogen. Their prowess stems from the intricate H-cluster, combining a [Fe4 S4 ] center with a binuclear iron center ([2Fe]H ). In the latter, each iron atom is coordinated by a CO and CN ligand, connected by a CO and an azadithiolate ligand. The synthesis of this active site involves a unique multiprotein assembly, featuring radical SAM proteins HydG and HydE. HydG initiates the transformation of L-tyrosine into cyanide and carbon monoxide to generate complex B, which is subsequently transferred to HydE to continue the biosynthesis of the [2Fe]H -subcluster. Due to its instability, complex B isolation for structural or spectroscopic characterization has been elusive thus far. Nevertheless, the use of a biomimetic analogue of complex B allowed circumvention of the need for the HydG protein during in vitro functional investigations, implying a similar structure for complex B. Herein, we used the HydE protein as a nanocage to encapsulate and stabilize the complex B product generated by HydG. Using X-ray crystallography, we successfully determined its structure at 1.3 Å resolution. Furthermore, we demonstrated that complex B is directly transferred from HydG to HydE, thus not being released into the solution post-synthesis, highlighting a transient interaction between the two proteins.
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Affiliation(s)
- Juneina Omeiri
- Univ. Grenoble-Alpes, CEA, CNRS, IBS, Metalloproteins Unit, 38000, Grenoble, France
| | - Lydie Martin
- Univ. Grenoble-Alpes, CEA, CNRS, IBS, Metalloproteins Unit, 38000, Grenoble, France
| | - Anthony Usclat
- Univ. Grenoble-Alpes, CEA, CNRS, IBS, Metalloproteins Unit, 38000, Grenoble, France
| | - Mickael V Cherrier
- Univ. Grenoble-Alpes, CEA, CNRS, IBS, Metalloproteins Unit, 38000, Grenoble, France
| | - Yvain Nicolet
- Univ. Grenoble-Alpes, CEA, CNRS, IBS, Metalloproteins Unit, 38000, Grenoble, France
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4
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Villarreal DG, Rao G, Tao L, Liu L, Rauchfuss TB, Britt RD. Characterizing the Biosynthesis of the [Fe(II)(CN)(CO) 2(cysteinate)] - Organometallic Product of the Radical-SAM Enzyme HydG by EPR and Mössbauer Spectroscopy. J Phys Chem B 2023; 127:9295-9302. [PMID: 37861415 DOI: 10.1021/acs.jpcb.3c05495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2023]
Abstract
[FeFe]-hydrogenases employ a catalytic H-cluster, consisting of a [4Fe-4S]H cluster linked to a [2Fe]H subcluster with CO, CN- ligands, and an azadithiolate bridge, which mediates the rapid redox interconversion of H+ and H2. In the biosynthesis of this H-cluster active site, the radical S-adenosyl-l-methionine (radical SAM, RS) enzyme HydG plays the crucial role of generating an organometallic [Fe(II)(CN)(CO)2(cysteinate)]- product that is en route to forming the H-cluster. Here, we report direct observation of this diamagnetic organometallic Fe(II) complex through Mössbauer spectroscopy, revealing an isomer shift of δ = 0.10 mm s-1 and quadrupole splitting of ΔEQ = 0.66 mm s-1. These Mössbauer values are a change from the starting values of δ = 1.15 mm s-1 and ΔEQ = 3.23 mm s-1 for the ferrous "dangler" Fe in HydG. These values of the observed product complex B are in good agreement with Mössbauer parameters for the low-spin Fe2+ ions in synthetic analogues, such as 57Fe Syn-B, which we report here. These results highlight the essential role that HydG plays in converting a resting-state high-spin Fe(II) to a low-spin organometallic Fe(II) product that can be transferred to the downstream maturase enzymes.
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Affiliation(s)
- David G Villarreal
- Department of Chemistry, University of California Davis, Davis, California 95616, United States
| | - Guodong Rao
- Department of Chemistry, University of California Davis, Davis, California 95616, United States
| | - Lizhi Tao
- Department of Chemistry, University of California Davis, Davis, California 95616, United States
| | - Liang Liu
- School of Chemical Sciences, University of Illinois at Urbana─Champaign, Urbana, Illinois 61801, United States
| | - Thomas B Rauchfuss
- School of Chemical Sciences, University of Illinois at Urbana─Champaign, Urbana, Illinois 61801, United States
| | - R David Britt
- Department of Chemistry, University of California Davis, Davis, California 95616, United States
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5
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Rao G, Yu X, Zhang Y, Rauchfuss TB, Britt RD. Fully Refined Semisynthesis of the [FeFe] Hydrogenase H-Cluster. Biochemistry 2023; 62:2868-2877. [PMID: 37691492 DOI: 10.1021/acs.biochem.3c00393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
[FeFe] hydrogenases contain a 6-Fe cofactor that serves as the active site for efficient redox interconversion between H2 and protons. The biosynthesis of the so-called H-cluster involves unusual enzymatic reactions that synthesize organometallic Fe complexes containing azadithiolate, CO, and CN- ligands. We have previously demonstrated that specific synthetic [Fe(CO)x(CN)y] complexes can be used to functionally replace proposed Fe intermediates in the maturation reaction. Here, we report the results from performing such cluster semisynthesis in the context of a recent fully defined cluster maturation procedure, which eliminates unknown components previously employed from Escherichia coli cell lysate and demonstrate this provides a concise route to H-cluster synthesis. We show that formaldehyde can be used as a simple reagent as the carbon source of the bridging adt ligand of H-cluster in lieu of serine/serine hydroxymethyltransferase. In addition to the actual H-cluster, we observe the formation of several H-cluster-like species, the identities of which are probed by cryogenic photolysis combined with EPR/ENDOR spectroscopy.
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Affiliation(s)
- Guodong Rao
- Department of Chemistry, University of California, Davis, Davis, California 95616, United States
| | - Xin Yu
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61820, United States
| | - Yu Zhang
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61820, United States
| | - Thomas B Rauchfuss
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61820, United States
| | - R David Britt
- Department of Chemistry, University of California, Davis, Davis, California 95616, United States
- Miller Institute for Basic Research in Science, University of California, Berkeley, Berkeley, California 94720, United States
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6
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Balci B, O'Neill RD, Shepard EM, Pagnier A, Marlott A, Mock MT, Broderick WE, Broderick JB. Semisynthetic maturation of [FeFe]-hydrogenase using [Fe 2(μ-SH) 2(CN) 2(CO) 4] 2-: key roles for HydF and GTP. Chem Commun (Camb) 2023. [PMID: 37376915 DOI: 10.1039/d3cc02169f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/29/2023]
Abstract
Here we describe maturation of the [FeFe]-hydrogenase from its [4Fe-4S]-bound precursor state by using the synthetic complex [Fe2(μ-SH)2(CN)2(CO)4]2- together with HydF and components of the glycine cleavage system, but in the absence of the maturases HydE and HydG. This semisynthetic and fully-defined maturation provides new insights into the nature of H-cluster biosynthesis.
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Affiliation(s)
- Batuhan Balci
- Department of Chemistry & Biochemistry, Montana State University, Bozeman, MT 59717, USA.
| | - Roark D O'Neill
- Department of Chemistry & Biochemistry, Montana State University, Bozeman, MT 59717, USA.
| | - Eric M Shepard
- Department of Chemistry & Biochemistry, Montana State University, Bozeman, MT 59717, USA.
| | - Adrien Pagnier
- Department of Chemistry & Biochemistry, Montana State University, Bozeman, MT 59717, USA.
| | - Alexander Marlott
- Department of Chemistry & Biochemistry, Montana State University, Bozeman, MT 59717, USA.
| | - Michael T Mock
- Department of Chemistry & Biochemistry, Montana State University, Bozeman, MT 59717, USA.
| | - William E Broderick
- Department of Chemistry & Biochemistry, Montana State University, Bozeman, MT 59717, USA.
| | - Joan B Broderick
- Department of Chemistry & Biochemistry, Montana State University, Bozeman, MT 59717, USA.
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7
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Sidabras JW, Stripp ST. A personal account on 25 years of scientific literature on [FeFe]-hydrogenase. J Biol Inorg Chem 2023; 28:355-378. [PMID: 36856864 DOI: 10.1007/s00775-023-01992-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Accepted: 01/25/2023] [Indexed: 03/02/2023]
Abstract
[FeFe]-hydrogenases are gas-processing metalloenzymes that catalyze H2 oxidation and proton reduction (H2 release) in microorganisms. Their high turnover frequencies and lack of electrical overpotential in the hydrogen conversion reaction has inspired generations of biologists, chemists, and physicists to explore the inner workings of [FeFe]-hydrogenase. Here, we revisit 25 years of scientific literature on [FeFe]-hydrogenase and propose a personal account on 'must-read' research papers and review article that will allow interested scientists to follow the recent discussions on catalytic mechanism, O2 sensitivity, and the in vivo synthesis of the active site cofactor with its biologically uncommon ligands carbon monoxide and cyanide. Focused on-but not restricted to-structural biology and molecular biophysics, we highlight future directions that may inspire young investigators to pursue a career in the exciting and competitive field of [FeFe]-hydrogenase research.
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Affiliation(s)
- Jason W Sidabras
- Department of Biophysics, Medical College of Wisconsin, 8701 Watertown Plank Rd, Milwaukee, WI, USA, 53226.
| | - Sven T Stripp
- Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195, Berlin, Germany.
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8
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Lorenzi M, Gamache MT, Redman HJ, Land H, Senger M, Berggren G. Light-Driven [FeFe] Hydrogenase Based H 2 Production in E. coli: A Model Reaction for Exploring E. coli Based Semiartificial Photosynthetic Systems. ACS SUSTAINABLE CHEMISTRY & ENGINEERING 2022; 10:10760-10767. [PMID: 36035441 PMCID: PMC9400101 DOI: 10.1021/acssuschemeng.2c03657] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 08/08/2022] [Indexed: 06/01/2023]
Abstract
Biohybrid technologies like semiartificial photosynthesis are attracting increased attention, as they enable the combination of highly efficient synthetic light-harvesters with the self-healing and outstanding performance of biocatalysis. However, such systems are intrinsically complex, with multiple interacting components. Herein, we explore a whole-cell photocatalytic system for hydrogen (H2) gas production as a model system for semiartificial photosynthesis. The employed whole-cell photocatalytic system is based on Escherichia coli cells heterologously expressing a highly efficient, but oxygen-sensitive, [FeFe] hydrogenase. The system is driven by the organic photosensitizer eosin Y under broad-spectrum white light illumination. The direct involvement of the [FeFe] hydrogenase in the catalytic reaction is verified spectroscopically. We also observe that E. coli provides protection against O2 damage, underscoring the suitability of this host organism for oxygen-sensitive enzymes in the development of (photo) catalytic biohybrid systems. Moreover, the study shows how factorial experimental design combined with analysis of variance (ANOVA) can be employed to identify relevant variables, as well as their interconnectivity, on both overall catalytic performance and O2 tolerance.
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Affiliation(s)
- Marco Lorenzi
- Department
of Chemistry - Ångström, Molecular Biomimetics, Uppsala University, Lägerhyddsvägen 1, 75120 Uppsala, Sweden
| | - Mira T. Gamache
- Department
of Chemistry - Ångström, Molecular Biomimetics, Uppsala University, Lägerhyddsvägen 1, 75120 Uppsala, Sweden
| | - Holly J. Redman
- Department
of Chemistry - Ångström, Molecular Biomimetics, Uppsala University, Lägerhyddsvägen 1, 75120 Uppsala, Sweden
| | - Henrik Land
- Department
of Chemistry - Ångström, Molecular Biomimetics, Uppsala University, Lägerhyddsvägen 1, 75120 Uppsala, Sweden
| | - Moritz Senger
- Department
of Chemistry - Ångström, Physical Chemistry, Uppsala University, Lägerhyddsvägen 1, 75120 Uppsala, Sweden
| | - Gustav Berggren
- Department
of Chemistry - Ångström, Molecular Biomimetics, Uppsala University, Lägerhyddsvägen 1, 75120 Uppsala, Sweden
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9
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Genome-Scale Mining of Acetogens of the Genus Clostridium Unveils Distinctive Traits in [FeFe]- and [NiFe]-Hydrogenase Content and Maturation. Microbiol Spectr 2022; 10:e0101922. [PMID: 35735976 PMCID: PMC9431212 DOI: 10.1128/spectrum.01019-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Knowledge of the organizational and functional properties of hydrogen metabolism is pivotal to the construction of a framework supportive of a hydrogen-fueled low-carbon economy. Hydrogen metabolism relies on the mechanism of action of hydrogenases. In this study, we investigated the genomes of several industrially relevant acetogens of the genus Clostridium (C. autoethanogenum, C. ljungdahlii, C. carboxidivorans, C. drakei, C. scatologenes, C. coskatii, C. ragsdalei, C. sp. AWRP) to systematically identify their intriguingly diversified hydrogenases’ repertoire. An entirely computational annotation pipeline unveiled common and strain-specific traits in the functional content of [NiFe]- and [FeFe]-hydrogenases. Hydrogenases were identified and categorized into functionally distinct classes by the combination of sequence homology, with respect to a database of curated nonredundant hydrogenases, with the analysis of sequence patterns characteristic of the mode of action of [FeFe]- and [NiFe]-hydrogenases. The inspection of the genes in the neighborhood of the catalytic subunits unveiled a wide agreement between their genomic arrangement and the gene organization templates previously developed for the predicted hydrogenase classes. Subunits’ characterization of the identified hydrogenases allowed us to glean some insights on the redox cofactor-binding determinants in the diaphorase subunits of the electron-bifurcating [FeFe]-hydrogenases. Finally, the reliability of the inferred hydrogenases was corroborated by the punctual analysis of the maturation proteins necessary for the biosynthesis of [NiFe]- and [FeFe]-hydrogenases. IMPORTANCE Mastering hydrogen metabolism can support a sustainable carbon-neutral economy. Of the many microorganisms metabolizing hydrogen, acetogens of the genus Clostridium are appealing, with some of them already in usage as industrial workhorses. Having provided detailed information on the hydrogenase content of an unprecedented number of clostridial acetogens at the gene level, our study represents a valuable knowledge base to deepen our understanding of hydrogenases’ functional specificity and/or redundancy and to develop a large array of biotechnological processes. We also believe our study could serve as a basis for future strain-engineering approaches, acting at the hydrogenases’ level or at the level of their maturation proteins. On the other side, the wealth of functional elements discussed in relation to the identified hydrogenases is worthy of further investigation by biochemical and structural studies to ultimately lead to the usage of these enzymes as valuable catalysts.
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10
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Pagnier A, Balci B, Shepard EM, Yang H, Warui DM, Impano S, Booker SJ, Hoffman BM, Broderick WE, Broderick JB. [FeFe]-Hydrogenase: Defined Lysate-Free Maturation Reveals a Key Role for Lipoyl-H-Protein in DTMA Ligand Biosynthesis. Angew Chem Int Ed Engl 2022; 61:e202203413. [PMID: 35319808 PMCID: PMC9117470 DOI: 10.1002/anie.202203413] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Indexed: 11/09/2022]
Abstract
Maturation of [FeFe]-hydrogenase (HydA) involves synthesis of a CO, CN- , and dithiomethylamine (DTMA)-coordinated 2Fe subcluster that is inserted into HydA to make the active hydrogenase. This process requires three maturation enzymes: the radical S-adenosyl-l-methionine (SAM) enzymes HydE and HydG, and the GTPase HydF. In vitro maturation with purified maturation enzymes has been possible only when clarified cell lysate was added, with the lysate presumably providing essential components for DTMA synthesis and delivery. Here we report maturation of [FeFe]-hydrogenase using a fully defined system that includes components of the glycine cleavage system (GCS), but no cell lysate. Our results reveal for the first time an essential role for the aminomethyl-lipoyl-H-protein of the GCS in hydrogenase maturation and the synthesis of the DTMA ligand of the H-cluster. In addition, we show that ammonia is the source of the bridgehead nitrogen of DTMA.
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Affiliation(s)
- Adrien Pagnier
- Department of Chemistry & Biochemistry, Montana State University, Bozeman, MT 59717, USA
| | - Batuhan Balci
- Department of Chemistry & Biochemistry, Montana State University, Bozeman, MT 59717, USA
| | - Eric M Shepard
- Department of Chemistry & Biochemistry, Montana State University, Bozeman, MT 59717, USA
| | - Hao Yang
- Department of Chemistry, Northwestern University, Evanston, IL 60208, USA
| | - Douglas M Warui
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA
| | - Stella Impano
- Department of Chemistry & Biochemistry, Montana State University, Bozeman, MT 59717, USA
| | - Squire J Booker
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Brian M Hoffman
- Department of Chemistry, Northwestern University, Evanston, IL 60208, USA
| | - William E Broderick
- Department of Chemistry & Biochemistry, Montana State University, Bozeman, MT 59717, USA
| | - Joan B Broderick
- Department of Chemistry & Biochemistry, Montana State University, Bozeman, MT 59717, USA
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11
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Tachezy J, Makki A, Hrdý I. The hydrogenosomes of Trichomonas vaginalis. J Eukaryot Microbiol 2022; 69:e12922. [PMID: 35567536 DOI: 10.1111/jeu.12922] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
This review is dedicated to the 50th anniversary of the discovery of hydrogenosomes by Miklós Müller and Donald Lindmark, which we will celebrate the following year. It was a long journey from the first observation of enigmatic rows of granules in trichomonads at the end of the 19th century to their first biochemical characterization in 1973. The key experiments by Müller and Lindmark revealed that the isolated granules contain hydrogen-producing hydrogenase, similar to some anaerobic bacteria-a discovery that gave birth to the field of hydrogenosomes. It is also important to acknowledge the parallel work of the team of Apolena Čerkasovová, Jiří Čerkasov, and Jaroslav Kulda, who demonstrated that these granules, similar to mitochondria, produce ATP. However, the evolutionary origin of hydrogenosomes remained enigmatic until the turn of the millennium, when it was finally accepted that hydrogenosomes and mitochondria evolved from a common ancestor. After a historical introduction, the review provides an overview of hydrogenosome biogenesis, hydrogenosomal protein import, and the relationship between the peculiar structure of membrane translocases and its low inner membrane potential due to the lack of respiratory complexes. Next, it summarizes the current state of knowledge on energy metabolism, the oxygen defense system, and iron/sulfur cluster assembly.
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Affiliation(s)
- Jan Tachezy
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Průmyslová 595, 25242 Vestec, Czech Republic
| | - Abhijith Makki
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Průmyslová 595, 25242 Vestec, Czech Republic
| | - Ivan Hrdý
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Průmyslová 595, 25242 Vestec, Czech Republic
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12
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Pagnier A, Balci B, Shepard EM, Yang H, Warui DM, Impano S, Booker SJ, Hoffman BM, Broderick WE, Broderick JB. [FeFe]‐Hydrogenase: Defined Lysate‐Free Maturation Reveals a Key Role for Lipoyl‐H‐Protein in DTMA Ligand Biosynthesis. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202203413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Adrien Pagnier
- Department of Chemistry & Biochemistry Montana State University Bozeman MT 59717 USA
| | - Batuhan Balci
- Department of Chemistry & Biochemistry Montana State University Bozeman MT 59717 USA
| | - Eric M. Shepard
- Department of Chemistry & Biochemistry Montana State University Bozeman MT 59717 USA
| | - Hao Yang
- Department of Chemistry Northwestern University Evanston IL 60208 USA
| | - Douglas M. Warui
- Department of Chemistry The Pennsylvania State University University Park PA 16802 USA
| | - Stella Impano
- Department of Chemistry & Biochemistry Montana State University Bozeman MT 59717 USA
| | - Squire J. Booker
- Department of Chemistry The Pennsylvania State University University Park PA 16802 USA
- Howard Hughes Medical Institute Chevy Chase MD 20815 USA
| | - Brian M. Hoffman
- Department of Chemistry Northwestern University Evanston IL 60208 USA
| | - William E. Broderick
- Department of Chemistry & Biochemistry Montana State University Bozeman MT 59717 USA
| | - Joan B. Broderick
- Department of Chemistry & Biochemistry Montana State University Bozeman MT 59717 USA
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13
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King SJ, Jerkovic A, Brown LJ, Petroll K, Willows RD. Synthetic biology for improved hydrogen production in Chlamydomonas reinhardtii. Microb Biotechnol 2022; 15:1946-1965. [PMID: 35338590 PMCID: PMC9249334 DOI: 10.1111/1751-7915.14024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 02/09/2022] [Accepted: 02/11/2022] [Indexed: 12/04/2022] Open
Abstract
Hydrogen is a clean alternative to fossil fuels. It has applications for electricity generation and transportation and is used for the manufacturing of ammonia and steel. However, today, H2 is almost exclusively produced from coal and natural gas. As such, methods to produce H2 that do not use fossil fuels need to be developed and adopted. The biological manufacturing of H2 may be one promising solution as this process is clean and renewable. Hydrogen is produced biologically via enzymes called hydrogenases. There are three classes of hydrogenases namely [FeFe], [NiFe] and [Fe] hydrogenases. The [FeFe] hydrogenase HydA1 from the model unicellular algae Chlamydomonas reinhardtii has been studied extensively and belongs to the A1 subclass of [FeFe] hydrogenases that have the highest turnover frequencies amongst hydrogenases (21,000 ± 12,000 H2 s−1 for CaHydA from Clostridium acetobutyliticum). Yet to date, limitations in C. reinhardtii H2 production pathways have hampered commercial scale implementation, in part due to O2 sensitivity of hydrogenases and competing metabolic pathways, resulting in low H2 production efficiency. Here, we describe key processes in the biogenesis of HydA1 and H2 production pathways in C. reinhardtii. We also summarize recent advancements of algal H2 production using synthetic biology and describe valuable tools such as high‐throughput screening (HTS) assays to accelerate the process of engineering algae for commercial biological H2 production.
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Affiliation(s)
- Samuel J King
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia
| | - Ante Jerkovic
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia
| | - Louise J Brown
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia
| | - Kerstin Petroll
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia
| | - Robert D Willows
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia
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14
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Lorenzi M, Ceccaldi P, Rodríguez-Maciá P, Redman HJ, Zamader A, Birrell JA, Mészáros LS, Berggren G. Stability of the H-cluster under whole-cell conditions-formation of an H trans-like state and its reactivity towards oxygen. J Biol Inorg Chem 2022; 27:345-355. [PMID: 35258679 PMCID: PMC8960641 DOI: 10.1007/s00775-022-01928-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 01/03/2022] [Indexed: 11/29/2022]
Abstract
Hydrogenases are metalloenzymes that catalyze the reversible oxidation of molecular hydrogen into protons and electrons. For this purpose, [FeFe]-hydrogenases utilize a hexanuclear iron cofactor, the H-cluster. This biologically unique cofactor provides the enzyme with outstanding catalytic activities, but it is also highly oxygen sensitive. Under in vitro conditions, oxygen stable forms of the H-cluster denoted Htrans and Hinact can be generated via treatment with sulfide under oxidizing conditions. Herein, we show that an Htrans-like species forms spontaneously under intracellular conditions on a time scale of hours, concurrent with the cells ceasing H2 production. Addition of cysteine or sulfide during the maturation promotes the formation of this H-cluster state. Moreover, it is found that formation of the observed Htrans-like species is influenced by both steric factors and proton transfer, underscoring the importance of outer coordination sphere effects on H-cluster reactivity.
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Affiliation(s)
- Marco Lorenzi
- Molecular Biomimetics, Department of Chemistry–Ångström Laboratory, Uppsala University, Box 523, 75120 Uppsala, Sweden
| | - Pierre Ceccaldi
- Molecular Biomimetics, Department of Chemistry–Ångström Laboratory, Uppsala University, Box 523, 75120 Uppsala, Sweden
- Present Address: Current Address: R&I Consultant, Home Office, Marseille, France
| | - Patricia Rodríguez-Maciá
- Department of Inorganic Spectroscopy, Max Planck Institute for Chemical Energy Conversion, Stiftstrasse 34-36, 45470 Mülheim an der Ruhr, Germany
- Present Address: Current address: Department of Chemistry, Inorganic Chemistry Laboratory, University of Oxford, South Parks Road, Oxford, OX1 3QR UK
| | - Holly Jayne Redman
- Molecular Biomimetics, Department of Chemistry–Ångström Laboratory, Uppsala University, Box 523, 75120 Uppsala, Sweden
| | - Afridi Zamader
- Molecular Biomimetics, Department of Chemistry–Ångström Laboratory, Uppsala University, Box 523, 75120 Uppsala, Sweden
- Laboratoire de Chimie et Biologie des Métaux, Université Grenoble Alpes, CNRS, CEA, 17 rue des Martyrs, 38054 Grenoble, France
| | - James A. Birrell
- Department of Inorganic Spectroscopy, Max Planck Institute for Chemical Energy Conversion, Stiftstrasse 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Livia S. Mészáros
- Molecular Biomimetics, Department of Chemistry–Ångström Laboratory, Uppsala University, Box 523, 75120 Uppsala, Sweden
| | - Gustav Berggren
- Molecular Biomimetics, Department of Chemistry–Ångström Laboratory, Uppsala University, Box 523, 75120 Uppsala, Sweden
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15
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Britt RD, Tao L, Rao G, Chen N, Wang LP. Proposed Mechanism for the Biosynthesis of the [FeFe] Hydrogenase H-Cluster: Central Roles for the Radical SAM Enzymes HydG and HydE. ACS BIO & MED CHEM AU 2022; 2:11-21. [PMID: 35187536 PMCID: PMC8855341 DOI: 10.1021/acsbiomedchemau.1c00035] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 10/08/2021] [Accepted: 10/11/2021] [Indexed: 01/05/2023]
Abstract
Radical S-adenosylmethionine (radical SAM or rSAM) enzymes use their S-adenosylmethionine cofactor bound to a unique Fe of a [4Fe-4S] cluster to generate the "hot" 5'-deoxyadenosyl radical, which drives highly selective radical reactions via specific interactions with a given rSAM enzyme's substrate. This Perspective focuses on the two rSAM enzymes involved in the biosynthesis of the organometallic H-cluster of [FeFe] hydrogenases. We present here a detailed sequential model initiated by HydG, which lyses a tyrosine substrate via a 5'-deoxyadenosyl H atom abstraction from those amino acid's amino group, initially producing dehydroglycine and an oxidobenzyl radical. In this model, two successive radical cascade reactions lead ultimately to the formation of HydG's product, a mononuclear Fe organometallic complex: [Fe(II)(CN)(CO)2(cysteinate)]-, with the iron originating from a unique "dangler" Fe coordinated by a cysteine ligand providing a sulfur bridge to another [4Fe-4S] auxiliary cluster in the enzyme. In turn, in this model, [Fe(II)(CN)(CO)2(cysteinate)]- is the substrate for HydE, the second rSAM enzyme in the biosynthetic pathway, which activates this mononuclear organometallic unit for dimerization, forming a [Fe2S2(CO)4(CN)2] precursor to the [2Fe] H component of the H-cluster, requiring only the completion of the bridging azadithiolate (SCH2NHCH2S) ligand. This model is built upon a foundation of data that incorporates cell-free synthesis, isotope sensitive spectroscopies, and the selective use of synthetic complexes substituting for intermediates in the enzymatic "assembly line". We discuss controversies pertaining to this model and some remaining open issues to be addressed by future work.
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Affiliation(s)
- R David Britt
- Department of Chemistry, University of California, Davis, Davis, California 95616, United States
| | - Lizhi Tao
- Department of Chemistry, University of California, Davis, Davis, California 95616, United States
| | - Guodong Rao
- Department of Chemistry, University of California, Davis, Davis, California 95616, United States
| | - Nanhao Chen
- Department of Chemistry, University of California, Davis, Davis, California 95616, United States
| | - Lee-Ping Wang
- Department of Chemistry, University of California, Davis, Davis, California 95616, United States
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16
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Nicolet Y, Cherrier MV, Amara P. Radical SAM Enzymes and Metallocofactor Assembly: A Structural Point of View. ACS BIO & MED CHEM AU 2022; 2:36-52. [PMID: 37102176 PMCID: PMC10114646 DOI: 10.1021/acsbiomedchemau.1c00044] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
This Review focuses on the structure-function relationship of radical S-adenosyl-l-methionine (SAM) enzymes involved in the assembly of metallocofactors corresponding to the active sites of [FeFe]-hydrogenase and nitrogenase [MoFe]-protein. It does not claim to correspond to an extensive review on the assembly machineries of these enzyme active sites, for which many good reviews are already available, but instead deals with the contribution of structural data to the understanding of their chemical mechanism (Buren et al. Chem. Rev.2020, 142 ( (25), ) 11006-11012; Britt et al. Chem. Sci.2020, 11 ( (38), ), 10313-10323). Hence, we will present the history and current knowledge about the radical SAM maturases HydE, HydG, and NifB as well as what, in our opinion, should be done in the near future to overcome the existing barriers in our understanding of this fascinating chemistry that intertwine organic radicals and organometallic complexes.
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Affiliation(s)
- Yvain Nicolet
- Univ. Grenoble Alpes, CEA, CNRS, IBS, Metalloproteins Unit, F-38000 Grenoble, France
| | - Mickael V. Cherrier
- Univ. Grenoble Alpes, CEA, CNRS, IBS, Metalloproteins Unit, F-38000 Grenoble, France
| | - Patricia Amara
- Univ. Grenoble Alpes, CEA, CNRS, IBS, Metalloproteins Unit, F-38000 Grenoble, France
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17
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Bigness A, Vaddypally S, Zdilla MJ, Mendoza-Cortes JL. Ubiquity of cubanes in bioinorganic relevant compounds. Coord Chem Rev 2022. [DOI: 10.1016/j.ccr.2021.214168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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18
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Smutná T, Dohnálková A, Sutak R, Narayanasamy RK, Tachezy J, Hrdý I. A cytosolic ferredoxin-independent hydrogenase possibly mediates hydrogen uptake in Trichomonas vaginalis. Curr Biol 2021; 32:124-135.e5. [PMID: 34762819 DOI: 10.1016/j.cub.2021.10.050] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 08/30/2021] [Accepted: 10/22/2021] [Indexed: 11/16/2022]
Abstract
Trichomonads, represented by the highly prevalent sexually transmitted human parasite Trichomonas vaginalis, are anaerobic eukaryotes with hydrogenosomes in the place of the standard mitochondria. Hydrogenosomes form indispensable FeS-clusters, synthesize ATP, and release molecular hydrogen as a waste product. Hydrogen formation is catalyzed by [FeFe] hydrogenase, the hallmark enzyme of all hydrogenosomes found in various eukaryotic anaerobes. Eukaryotic hydrogenases were originally thought to be exclusively localized within organelles, but today few eukaryotic anaerobes are known that possess hydrogenase in their cytosol. We identified a thus-far unknown hydrogenase in T. vaginalis cytosol that cannot use ferredoxin as a redox partner but can use cytochrome b5 as an electron acceptor. Trichomonads overexpressing the cytosolic hydrogenase, while maintaining the carbon flux through hydrogenosomes, show decreased excretion of hydrogen and increased excretion of methylated alcohols, suggesting that the cytosolic hydrogenase uses the hydrogen gas as a source of reducing power for the reactions occurring in the cytoplasm and thus accounts for the overall redox balance. This is the first evidence of hydrogen uptake in a eukaryote, although further work is needed to confirm it. Assembly of the catalytic center of [FeFe] hydrogenases (H-cluster) requires the activity of three dedicated maturases, and these proteins in T. vaginalis are exclusively localized in hydrogenosomes, where they participate in the maturation of organellar hydrogenases. Despite the different subcellular localization of cytosolic hydrogenase and maturases, the H-cluster is present in the cytosolic enzyme, suggesting the existence of an alternative mechanism of H-cluster assembly.
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Affiliation(s)
- Tamara Smutná
- Charles University, Faculty of Science, Department of Parasitology, BIOCEV, Vestec 252 50, Czech Republic
| | - Alena Dohnálková
- Charles University, Faculty of Science, Department of Parasitology, BIOCEV, Vestec 252 50, Czech Republic
| | - Róbert Sutak
- Charles University, Faculty of Science, Department of Parasitology, BIOCEV, Vestec 252 50, Czech Republic
| | - Ravi Kumar Narayanasamy
- Charles University, Faculty of Science, Department of Parasitology, BIOCEV, Vestec 252 50, Czech Republic
| | - Jan Tachezy
- Charles University, Faculty of Science, Department of Parasitology, BIOCEV, Vestec 252 50, Czech Republic
| | - Ivan Hrdý
- Charles University, Faculty of Science, Department of Parasitology, BIOCEV, Vestec 252 50, Czech Republic.
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19
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Chen N, Rao G, Britt RD, Wang LP. Quantum Chemical Study of a Radical Relay Mechanism for the HydG-Catalyzed Synthesis of a Fe(II)(CO) 2(CN)cysteine Precursor to the H-Cluster of [FeFe] Hydrogenase. Biochemistry 2021; 60:3016-3026. [PMID: 34569243 DOI: 10.1021/acs.biochem.1c00379] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The [FeFe] hydrogenase catalyzes the redox interconversion of protons and H2 with a Fe-S "H-cluster" employing CO, CN, and azadithiolate ligands to two Fe centers. The biosynthesis of the H-cluster is a highly interesting reaction carried out by a set of Fe-S maturase enzymes called HydE, HydF, and HydG. HydG, a member of the radical S-adenosylmethionine (rSAM) family, converts tyrosine, cysteine, and Fe(II) into an organometallic Fe(II)(CO)2(CN)cysteine "synthon", which serves as the substrate for HydE. Although key aspects of the HydG mechanism have been experimentally determined via isotope-sensitive spectroscopic methods, other important mechanistic questions have eluded experimental determination. Here, we use computational quantum chemistry to refine the mechanism of the HydG catalytic reaction. We utilize quantum mechanics/molecular mechanics simulations to investigate the reactions at the canonical Fe-S cluster, where a radical cleavage of the tyrosine substrate takes place and proceeds through a relay of radical intermediates to form HCN and a COO•- radical anion. We then carry out a broken-symmetry density functional theory study of the reactions at the unusual five-iron auxiliary Fe-S cluster, where two equivalents of CN- and COOH• coordinate to the fifth "dangler iron" in a series of substitution and redox reactions that yield the synthon as the final product for further processing by HydE.
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Affiliation(s)
- Nanhao Chen
- Department of Chemistry, University of California Davis, Davis, California 95616, United States
| | - Guodong Rao
- Department of Chemistry, University of California Davis, Davis, California 95616, United States
| | - R David Britt
- Department of Chemistry, University of California Davis, Davis, California 95616, United States
| | - Lee-Ping Wang
- Department of Chemistry, University of California Davis, Davis, California 95616, United States
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20
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Kosourov S, Böhm M, Senger M, Berggren G, Stensjö K, Mamedov F, Lindblad P, Allahverdiyeva Y. Photosynthetic hydrogen production: Novel protocols, promising engineering approaches and application of semi-synthetic hydrogenases. PHYSIOLOGIA PLANTARUM 2021; 173:555-567. [PMID: 33860946 DOI: 10.1111/ppl.13428] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 04/05/2021] [Indexed: 06/12/2023]
Abstract
Photosynthetic production of molecular hydrogen (H2 ) by cyanobacteria and green algae is a potential source of renewable energy. These organisms are capable of water biophotolysis by taking advantage of photosynthetic apparatus that links water oxidation at Photosystem II and reduction of protons to H2 downstream of Photosystem I. Although the process has a theoretical potential to displace fossil fuels, photosynthetic H2 production in its current state is not yet efficient enough for industrial applications due to a number of physiological, biochemical, and engineering barriers. This article presents a short overview of the metabolic pathways and enzymes involved in H2 photoproduction in cyanobacteria and green algae and our present understanding of the mechanisms of this process. We also summarize recent advances in engineering photosynthetic cell factories capable of overcoming the major barriers to efficient and sustainable H2 production.
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Affiliation(s)
- Sergey Kosourov
- Molecular Plant Biology, Department of Life Technologies, University of Turku, Turku, Finland
| | - Maximilian Böhm
- Molecular Biomimetics, Department of Chemistry-Ångström, Ångström Laboratory, Uppsala University, Uppsala, Sweden
| | - Moritz Senger
- Molecular Biomimetics, Department of Chemistry-Ångström, Ångström Laboratory, Uppsala University, Uppsala, Sweden
| | - Gustav Berggren
- Molecular Biomimetics, Department of Chemistry-Ångström, Ångström Laboratory, Uppsala University, Uppsala, Sweden
| | - Karin Stensjö
- Microbial Chemistry, Department of Chemistry-Ångström, Ångström Laboratory, Uppsala University, Uppsala, Sweden
| | - Fikret Mamedov
- Molecular Biomimetics, Department of Chemistry-Ångström, Ångström Laboratory, Uppsala University, Uppsala, Sweden
| | - Peter Lindblad
- Microbial Chemistry, Department of Chemistry-Ångström, Ångström Laboratory, Uppsala University, Uppsala, Sweden
| | - Yagut Allahverdiyeva
- Molecular Plant Biology, Department of Life Technologies, University of Turku, Turku, Finland
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21
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Feng JQ, Wang BJ. Super-exchange and exchange-enhanced reactivity in Fe4S4-mediated activation of SAM by radical SAM enzymes. CHINESE J CHEM PHYS 2021. [DOI: 10.1063/1674-0068/cjcp2108134] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Jian-qiang Feng
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Bin-ju Wang
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
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22
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Britt RD, Rauchfuss TB. Biosynthesis of the [FeFe] hydrogenase H-cluster via a synthetic [Fe(II)(CN)(CO) 2(cysteinate)] - complex. Dalton Trans 2021; 50:12386-12391. [PMID: 34545884 DOI: 10.1039/d1dt02258j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The H-cluster of [Fe-Fe] hydrogenase consists of a [4Fe]H subcluster linked by the sulfur of a cysteine residue to an organometallic [2Fe]H subcluster that utilizes terminal CO and CN ligands to each Fe along with a bridging CO and a bridging SCH2NHCH2S azadithiolate (adt) to catalyze proton reduction or hydrogen oxidation. Three Fe-S "maturase" proteins, HydE, HydF, and HydG, are responsible for the biosynthesis of the [2Fe]H subcluster and its incorporation into the hydrogenase enzyme to form this catalytically active H-cluster. We have proposed that HydG is a bifunctional enzyme that uses S-adenosylmethione (SAM) bound to a [4Fe-4S] cluster to lyse tyrosine via a transient 5'-deoxyadenosyl radical to produce CO and CN ligands to a unique cysteine-chelated Fe(II) that is linked to a second [4Fe-4S] cluster via the cysteine sulfur. In this "synthon model", after two cycles of tyrosine lysis, the product of HydG is completed: a [Fe(CN)(CO)2(cysteinate)]- organometallic unit that is vectored directly into the synthesis of the [2Fe]H sub-cluster. However our HydG-centric synthon model is not universally accepted, so further validation is important. In this Frontiers article, we discuss recent results using a synthetic "Syn-B" complex that donates [Fe(CN)(CO)2(cysteinate)]- units that match our proposed HydG product. Can Syn-B activate hydrogenase in the absence of HydG and its tyrosine substrate? If so, since Syn-B can be synthesized with specific magnetic nuclear isotopes and with chemical substitutions, its use could allow its enzymatic conversions on the route to the H-cluster to be monitored and modeled in fresh detail.
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Affiliation(s)
- R David Britt
- Department of Chemistry, University of California Davis, Davis, CA 95616, USA.
| | - Thomas B Rauchfuss
- School of Chemical Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA.
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23
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Feng J, Shaik S, Wang B. Spin‐Regulated Electron Transfer and Exchange‐Enhanced Reactivity in Fe
4
S
4
‐Mediated Redox Reaction of the Dph2 Enzyme During the Biosynthesis of Diphthamide. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202107008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Jianqiang Feng
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry College of Chemistry and Chemical Engineering Xiamen University Xiamen 361005 China
| | - Sason Shaik
- Institute of Chemistry The Hebrew University of Jerusalem Jerusalem 9190401 Israel
| | - Binju Wang
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry College of Chemistry and Chemical Engineering Xiamen University Xiamen 361005 China
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24
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Feng J, Shaik S, Wang B. Spin-Regulated Electron Transfer and Exchange-Enhanced Reactivity in Fe 4 S 4 -Mediated Redox Reaction of the Dph2 Enzyme During the Biosynthesis of Diphthamide. Angew Chem Int Ed Engl 2021; 60:20430-20436. [PMID: 34302311 DOI: 10.1002/anie.202107008] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Indexed: 11/06/2022]
Abstract
The [4Fe-4S]-dependent radical S-adenosylmethionine (SAM) proteins is one of large families of redox enzymes that are able to carry a panoply of challenging transformations. Despite the extensive studies of structure-function relationships of radical SAM (RS) enzymes, the electronic state-dependent reactivity of the [4Fe-4S] cluster in these enzymes remains elusive. Using combined MD simulations and QM/MM calculations, we deciphered the electronic state-dependent reactivity of the [4Fe-4S] cluster in Dph2, a key enzyme involved in the biosynthesis of diphthamide. Our calculations show that the reductive cleavage of the S-C(γ) bond is highly dependent on the electronic structure of [4Fe-4S]. Interestingly, the six electronic states can be classified into a low-energy and a high-energy groups, which are correlated with the net spin of Fe4 atom ligated to SAM. Due to the driving force of Fe4-C(γ) bonding, the net spin on the Fe4 moiety dictate the shift of the opposite spin electron from the Fe1-Fe2-Fe3 block to SAM. Such spin-regulated electron transfer results in the exchange-enhanced reactivity in the lower-energy group compared with those in the higher-energy group. This reactivity principle provides fundamental mechanistic insights into reactivities of [4Fe-4S] cluster in RS enzymes.
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Affiliation(s)
- Jianqiang Feng
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
| | - Sason Shaik
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, 9190401, Israel
| | - Binju Wang
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
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25
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Shepard EM, Impano S, Duffus BR, Pagnier A, Duschene KS, Betz JN, Byer AS, Galambas A, McDaniel EC, Watts H, McGlynn SE, Peters JW, Broderick WE, Broderick JB. HydG, the "dangler" iron, and catalytic production of free CO and CN -: implications for [FeFe]-hydrogenase maturation. Dalton Trans 2021; 50:10405-10422. [PMID: 34240096 DOI: 10.1039/d1dt01359a] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The organometallic H-cluster of the [FeFe]-hydrogenase consists of a [4Fe-4S] cubane bridged via a cysteinyl thiolate to a 2Fe subcluster ([2Fe]H) containing CO, CN-, and dithiomethylamine (DTMA) ligands. The H-cluster is synthesized by three dedicated maturation proteins: the radical SAM enzymes HydE and HydG synthesize the non-protein ligands, while the GTPase HydF serves as a scaffold for assembly of [2Fe]H prior to its delivery to the [FeFe]-hydrogenase containing the [4Fe-4S] cubane. HydG uses l-tyrosine as a substrate, cleaving it to produce p-cresol as well as the CO and CN- ligands to the H-cluster, although there is some question as to whether these are formed as free diatomics or as part of a [Fe(CO)2(CN)] synthon. Here we show that Clostridium acetobutylicum (C.a.) HydG catalyzes formation of multiple equivalents of free CO at rates comparable to those for CN- formation. Free CN- is also formed in excess molar equivalents over protein. A g = 8.9 EPR signal is observed for C.a. HydG reconstituted to load the 5th "dangler" iron of the auxiliary [4Fe-4S][FeCys] cluster and is assigned to this "dangler-loaded" cluster state. Free CO and CN- formation and the degree of activation of [FeFe]-hydrogenase all occur regardless of dangler loading, but are increased 10-35% in the dangler-loaded HydG; this indicates the dangler iron is not essential to this process but may affect relevant catalysis. During HydG turnover in the presence of myoglobin, the g = 8.9 signal remains unchanged, indicating that a [Fe(CO)2(CN)(Cys)] synthon is not formed at the dangler iron. Mutation of the only protein ligand to the dangler iron, H272, to alanine nearly completely abolishes both free CO formation and hydrogenase activation, however results show this is not due solely to the loss of the dangler iron. In experiments with wild type and H272A HydG, and with different degrees of dangler loading, we observe a consistent correlation between free CO/CN- formation and hydrogenase activation. Taken in full, our results point to free CO/CN-, but not an [Fe(CO)2(CN)(Cys)] synthon, as essential species in hydrogenase maturation.
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Affiliation(s)
- Eric M Shepard
- Department of Chemistry & Biochemistry, Montana State University, Bozeman, MT 59717, USA.
| | - Stella Impano
- Department of Chemistry & Biochemistry, Montana State University, Bozeman, MT 59717, USA.
| | - Benjamin R Duffus
- Department of Chemistry & Biochemistry, Montana State University, Bozeman, MT 59717, USA.
| | - Adrien Pagnier
- Department of Chemistry & Biochemistry, Montana State University, Bozeman, MT 59717, USA.
| | - Kaitlin S Duschene
- Department of Chemistry & Biochemistry, Montana State University, Bozeman, MT 59717, USA.
| | - Jeremiah N Betz
- Department of Chemistry & Biochemistry, Montana State University, Bozeman, MT 59717, USA.
| | - Amanda S Byer
- Department of Chemistry & Biochemistry, Montana State University, Bozeman, MT 59717, USA.
| | - Amanda Galambas
- Department of Chemistry & Biochemistry, Montana State University, Bozeman, MT 59717, USA.
| | - Elizabeth C McDaniel
- Department of Chemistry & Biochemistry, Montana State University, Bozeman, MT 59717, USA.
| | - Hope Watts
- Department of Chemistry & Biochemistry, Montana State University, Bozeman, MT 59717, USA.
| | - Shawn E McGlynn
- Earth-Life Science Institute, Tokyo Institute of Technology, Ookayama, Meguro-ku, Tokyo 152-8550, Japan
| | - John W Peters
- Institute of Biological Chemistry, Washington State University, Pullman, WA 99163, USA
| | - William E Broderick
- Department of Chemistry & Biochemistry, Montana State University, Bozeman, MT 59717, USA.
| | - Joan B Broderick
- Department of Chemistry & Biochemistry, Montana State University, Bozeman, MT 59717, USA.
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Rohac R, Martin L, Liu L, Basu D, Tao L, Britt RD, Rauchfuss TB, Nicolet Y. Crystal Structure of the [FeFe]-Hydrogenase Maturase HydE Bound to Complex-B. J Am Chem Soc 2021; 143:8499-8508. [PMID: 34048236 DOI: 10.1021/jacs.1c03367] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
[FeFe]-hydrogenases use a unique organometallic complex, termed the H cluster, to reversibly convert H2 into protons and low-potential electrons. It can be best described as a [Fe4S4] cluster coupled to a unique [2Fe]H center where the reaction actually takes place. The latter corresponds to two iron atoms, each of which is bound by one CN- ligand and one CO ligand. The two iron atoms are connected by a unique azadithiolate molecule (-S-CH2-NH-CH2-S-) and an additional bridging CO. This [2Fe]H center is built stepwise thanks to the well-orchestrated action of maturating enzymes that belong to the Hyd machinery. Among them, HydG converts l-tyrosine into CO and CN- to produce a unique l-cysteine-Fe(CO)2CN species termed complex-B. Very recently, HydE was shown to perform radical-based chemistry using synthetic complex-B as a substrate. Here we report the high-resolution crystal structure that establishes the identity of the complex-B-bound HydE. By triggering the reaction prior to crystallization, we trapped a new five-coordinate Fe species, supporting the proposal that HydE performs complex modifications of complex-B to produce a monomeric "SFe(CO)2CN" precursor to the [2Fe]H center. Substrate access, product release, and intermediate transfer are also discussed.
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Affiliation(s)
- Roman Rohac
- Univ. Grenoble Alpes, CEA, CNRS, IBS, Metalloproteins Unit, F-38000 Grenoble, France
| | - Lydie Martin
- Univ. Grenoble Alpes, CEA, CNRS, IBS, Metalloproteins Unit, F-38000 Grenoble, France
| | - Liang Liu
- School of Chemical Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Debashis Basu
- School of Chemical Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Lizhi Tao
- Department of Chemistry, University of California-Davis, Davis, California 95616, United States
| | - R David Britt
- Department of Chemistry, University of California-Davis, Davis, California 95616, United States
| | - Thomas B Rauchfuss
- School of Chemical Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Yvain Nicolet
- Univ. Grenoble Alpes, CEA, CNRS, IBS, Metalloproteins Unit, F-38000 Grenoble, France
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Khushvakov J, Nussbaum R, Cadoux C, Duan J, Stripp ST, Milton RD. Following Electroenzymatic Hydrogen Production by Rotating Ring-Disk Electrochemistry and Mass Spectrometry*. Angew Chem Int Ed Engl 2021; 60:10001-10006. [PMID: 33630389 DOI: 10.1002/anie.202100863] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Indexed: 11/06/2022]
Abstract
Gas-processing metalloenzymes are of interest to future bio- and bioinspired technologies. Of particular importance are hydrogenases and nitrogenases, which both produce molecular hydrogen (H2 ) from proton (H+ ) reduction. Herein, we report on the use of rotating ring-disk electrochemistry (RRDE) and mass spectrometry (MS) to follow the production of H2 and isotopes produced from deuteron (D+ ) reduction (HD and D2 ) using the [FeFe]-hydrogenase from Clostridium pasteurianum, a model hydrogen-evolving metalloenzyme. This facilitates enzymology studies independent of non-innocent chemical reductants. We anticipate that these approaches will be of value in resolving the catalytic mechanisms of H2 -producing metalloenzymes and the design of bioinspired catalysts for H2 production and N2 fixation.
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Affiliation(s)
- Jaloliddin Khushvakov
- Department of Inorganic and Analytical Chemistry, University of Geneva, Quai Ernest-Ansermet 30, 1211, Geneva 4, Switzerland
| | - Robin Nussbaum
- Department of Inorganic and Analytical Chemistry, University of Geneva, Quai Ernest-Ansermet 30, 1211, Geneva 4, Switzerland
| | - Cécile Cadoux
- Department of Inorganic and Analytical Chemistry, University of Geneva, Quai Ernest-Ansermet 30, 1211, Geneva 4, Switzerland
| | - Jifu Duan
- Faculty of Biology and Biotechnology, Photobiotechnology, Ruhr-Universität Bochum, Universitätsstrasse 150, 44801, Bochum, Germany
| | - Sven T Stripp
- Department of Physics, Experimental Molecular Biophysics, Freie Universität Berlin, 10623, Berlin, Germany
| | - Ross D Milton
- Department of Inorganic and Analytical Chemistry, University of Geneva, Quai Ernest-Ansermet 30, 1211, Geneva 4, Switzerland
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28
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Khushvakov J, Nussbaum R, Cadoux C, Duan J, Stripp ST, Milton RD. Untersuchung elektroenzymatischer H
2
‐Produktion mithilfe von Rotierende‐Ring‐Scheiben‐Elektrochemie und Massenspektrometrie**. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202100863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Jaloliddin Khushvakov
- Department of Inorganic and Analytical Chemistry University of Geneva Quai Ernest-Ansermet 30 1211 Geneva 4 Schweiz
| | - Robin Nussbaum
- Department of Inorganic and Analytical Chemistry University of Geneva Quai Ernest-Ansermet 30 1211 Geneva 4 Schweiz
| | - Cécile Cadoux
- Department of Inorganic and Analytical Chemistry University of Geneva Quai Ernest-Ansermet 30 1211 Geneva 4 Schweiz
| | - Jifu Duan
- Faculty of Biology and Biotechnology, Photobiotechnology Ruhr-Universität Bochum Universitätsstraße 150 44801 Bochum Deutschland
| | - Sven T. Stripp
- Department of Physics, Experimental Molecular Biophysics Freie Universität Berlin 10623 Berlin Deutschland
| | - Ross D. Milton
- Department of Inorganic and Analytical Chemistry University of Geneva Quai Ernest-Ansermet 30 1211 Geneva 4 Schweiz
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29
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Occurrence, Evolution and Specificities of Iron-Sulfur Proteins and Maturation Factors in Chloroplasts from Algae. Int J Mol Sci 2021; 22:ijms22063175. [PMID: 33804694 PMCID: PMC8003979 DOI: 10.3390/ijms22063175] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Revised: 02/25/2021] [Accepted: 03/17/2021] [Indexed: 01/08/2023] Open
Abstract
Iron-containing proteins, including iron-sulfur (Fe-S) proteins, are essential for numerous electron transfer and metabolic reactions. They are present in most subcellular compartments. In plastids, in addition to sustaining the linear and cyclic photosynthetic electron transfer chains, Fe-S proteins participate in carbon, nitrogen, and sulfur assimilation, tetrapyrrole and isoprenoid metabolism, and lipoic acid and thiamine synthesis. The synthesis of Fe-S clusters, their trafficking, and their insertion into chloroplastic proteins necessitate the so-called sulfur mobilization (SUF) protein machinery. In the first part, we describe the molecular mechanisms that allow Fe-S cluster synthesis and insertion into acceptor proteins by the SUF machinery and analyze the occurrence of the SUF components in microalgae, focusing in particular on the green alga Chlamydomonas reinhardtii. In the second part, we describe chloroplastic Fe-S protein-dependent pathways that are specific to Chlamydomonas or for which Chlamydomonas presents specificities compared to terrestrial plants, putting notable emphasis on the contribution of Fe-S proteins to chlorophyll synthesis in the dark and to the fermentative metabolism. The occurrence and evolutionary conservation of these enzymes and pathways have been analyzed in all supergroups of microalgae performing oxygenic photosynthesis.
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Abstract
The need to safeguard our planet by reducing carbon dioxide emissions has led to a significant development of research in the field of alternative energy sources. Hydrogen has proved to be the most promising molecule, as a fuel, due to its low environmental impact. Even if various methods already exist for producing hydrogen, most of them are not sustainable. Thus, research focuses on the biological sector, studying microalgae, and other microorganisms’ ability to produce this precious molecule in a natural way. In this review, we provide a description of the biochemical and molecular processes for the production of biohydrogen and give a general overview of one of the most interesting technologies in which hydrogen finds application for electricity production: fuel cells.
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31
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Li Z, Gu J, Ding J, Ren N, Xing D. Molecular mechanism of ethanol-H 2 co-production fermentation in anaerobic acidogenesis: Challenges and perspectives. Biotechnol Adv 2020; 46:107679. [PMID: 33316366 DOI: 10.1016/j.biotechadv.2020.107679] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 12/04/2020] [Accepted: 12/07/2020] [Indexed: 12/29/2022]
Abstract
Ethanol-type fermentation (ETF) is one of three fermentation types during the acidogenesis of the anaerobic biological treatment. Ethanoligenens, a representative genus of ETF, displays acidophilic, autoaggregative, and ethanol-H2 co-producing characteristics and facilitates subsequent methanogenesis. Here, the latest advances in the molecular mechanisms of the metabolic regulation of ethanol-H2 co-producing bacteria based on multi-omics studies were comprehensively reviewed. Comparative genomics demonstrated a low genetic similarity between Ethanoligenens and other hydrogen-producing genera. FeFe‑hydrogenases (FeFe-H2ases) and pyruvate ferredoxin oxidoreductase (PFOR) played critical roles in the ethanol-H2 co-metabolic pathway of Ethanoligenens. Global transcriptome analysis revealed that highly expressed [FeFe]-H2ases and ferredoxins drove hydrogen production by Ethanoligenens at low pH conditions (4.0-4.5). Quantitative proteomic analysis also proved that this genus resists acetic acid-induced intracellular acidification through the up-regulated expression of pyrimidine metabolism related proteins. The autoaggregation of Ethanoligenen facilitated its granulation with acetate-oxidizing bacteria in co-culture systems and mitigated a fast pH drop, providing a new approach for solving a pH imbalance and improving hydrogen production. In-depth studies of the regulatory mechanism underlying ethanol-H2 co-production metabolism and the syntrophic interactions of ethanol-H2 co-producing Ethanoligenens with other microorganisms will provide insights into the improvement of bioenergy recovery in anaerobic biotechnology. The coupling of ETF with other biotechnologies, which based on the regulation of electron flow direction, syntrophic interaction, and metabolic flux, can be potential strategies to enhance the cascade recovery of energy and resources.
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Affiliation(s)
- Zhen Li
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Jiayu Gu
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Jie Ding
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Nanqi Ren
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Defeng Xing
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China.
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32
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Britt RD, Rao G, Tao L. Biosynthesis of the catalytic H-cluster of [FeFe] hydrogenase: the roles of the Fe-S maturase proteins HydE, HydF, and HydG. Chem Sci 2020; 11:10313-10323. [PMID: 34123177 PMCID: PMC8162317 DOI: 10.1039/d0sc04216a] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 09/11/2020] [Indexed: 11/22/2022] Open
Abstract
[FeFe] hydrogenases carry out the redox interconversion of protons and molecular hydrogen (2H+ + 2e- ⇌ H2) at a complex Fe-S active site known as the H-cluster. The H-cluster consists of a [4Fe-4S] subcluster, denoted here as [4Fe]H, linked via a cysteine sulfur to an interesting organometallic [2Fe]H subcluster thought to be the subsite where the catalysis occurs. This [2Fe]H subcluster consists of two Fe atoms, linked with a bridging CO and a bridging SCH2NHCH2S azadithiolate (adt), with additional terminal CO and CN ligands bound to each Fe. Synthesizing such a complex organometallic unit is a fascinating problem in biochemistry, complicated by the toxic nature of both the CO and CN- species and the relative fragility of the azadithiolate bridge. It has been known for a number of years that this complex biosynthesis is carried out by a set of three essential Fe-S proteins, HydE, HydF, and HydG. HydF is a GTPase, while HydE and HydG are both members of the large family of radical S-adenosylmethionine (rSAM) enzymes. In this perspective we describe the history of research and discovery concerning these three Fe-S "maturase" proteins and describe recent evidence for a sequential biosynthetic pathway beginning with the synthesis of a mononuclear organometallic [Fe(ii)(CO)2CN(cysteine)] complex by the rSAM enzyme HydG and its subsequent activation by the second rSAM enzyme HydE to form a highly reactive Fe(i)(CO)2(CN)S species. In our model a pair of these Fe(i)(CO)2(CN)S units condense to form the [Fe(CO)2(CN)S]2 diamond core of the [2Fe]H cluster, requiring only the installation of the central CH2NHCH2 portion of the azadithiolate bridge, whose atoms are all sourced from the amino acid serine. This final step likely occurs with an interplay of HydE and HydF, the details of which yet remain to be elucidated.
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Affiliation(s)
- R David Britt
- Department of Chemistry, University of California, Davis Davis CA 95616 USA
| | - Guodong Rao
- Department of Chemistry, University of California, Davis Davis CA 95616 USA
| | - Lizhi Tao
- Department of Chemistry, University of California, Davis Davis CA 95616 USA
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33
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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: 7] [Impact Index Per Article: 1.8] [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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35
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Merino N, Kawai M, Boyd ES, Colman DR, McGlynn SE, Nealson KH, Kurokawa K, Hongoh Y. Single-Cell Genomics of Novel Actinobacteria With the Wood-Ljungdahl Pathway Discovered in a Serpentinizing System. Front Microbiol 2020; 11:1031. [PMID: 32655506 PMCID: PMC7325909 DOI: 10.3389/fmicb.2020.01031] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 04/27/2020] [Indexed: 01/04/2023] Open
Abstract
Serpentinite-hosted systems represent modern-day analogs of early Earth environments. In these systems, water-rock interactions generate highly alkaline and reducing fluids that can contain hydrogen, methane, and low-molecular-weight hydrocarbons-potent reductants capable of fueling microbial metabolism. In this study, we investigated the microbiota of Hakuba Happo hot springs (∼50°C; pH∼10.5-11), located in Nagano (Japan), which are impacted by the serpentinization process. Analysis of the 16S rRNA gene amplicon sequences revealed that the bacterial community comprises Nitrospirae (47%), "Parcubacteria" (19%), Deinococcus-Thermus (16%), and Actinobacteria (9%), among others. Notably, only 57 amplicon sequence variants (ASV) were detected, and fifteen of these accounted for 90% of the amplicons. Among the abundant ASVs, an early-branching, uncultivated actinobacterial clade identified as RBG-16-55-12 in the SILVA database was detected. Ten single-cell genomes (average pairwise nucleotide identity: 0.98-1.00; estimated completeness: 33-93%; estimated genome size: ∼2.3 Mb) that affiliated with this clade were obtained. Taxonomic classification using single copy genes indicates that the genomes belong to the actinobacterial class-level clade UBA1414 in the Genome Taxonomy Database. Based on metabolic pathway predictions, these actinobacteria are anaerobes, capable of glycolysis, dissimilatory nitrate reduction and CO2 fixation via the Wood-Ljungdahl (WL) pathway. Several other genomes within UBA1414 and two related class-level clades also encode the WL pathway, which has not yet been reported for the Actinobacteria phylum. For the Hakuba actinobacterium, the energy metabolism related to the WL pathway is likely supported by a combination of the Rnf complex, group 3b and 3d [NiFe]-hydrogenases, [FeFe]-hydrogenases, and V-type (H+/Na+ pump) ATPase. The genomes also harbor a form IV ribulose 1,5-bisphosphate carboxylase/oxygenase (RubisCO) complex, also known as a RubisCO-like protein, and contain signatures of interactions with viruses, including clustered regularly interspaced short palindromic repeat (CRISPR) regions and several phage integrases. This is the first report and detailed genome analysis of a bacterium within the Actinobacteria phylum capable of utilizing the WL pathway. The Hakuba actinobacterium is a member of the clade UBA1414/RBG-16-55-12, formerly within the group "OPB41." We propose to name this bacterium 'Candidatus Hakubanella thermoalkaliphilus.'
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Affiliation(s)
- Nancy Merino
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, Japan.,Department of Earth Sciences, University of Southern California, Los Angeles, CA, United States.,Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA, United States
| | - Mikihiko Kawai
- School of Life Sciences and Technology, Tokyo Institute of Technology, Tokyo, Japan.,Graduate School of Human and Environmental Studies, Kyoto University, Kyoto, Japan
| | - Eric S Boyd
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT, United States
| | - Daniel R Colman
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT, United States
| | - Shawn E McGlynn
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, Japan.,Biofunctional Catalyst Research Team, RIKEN Center for Sustainable Resource Science, Saitama, Japan.,Blue Marble Space Institute of Science, Seattle, WA, United States
| | - Kenneth H Nealson
- Department of Earth Sciences, University of Southern California, Los Angeles, CA, United States
| | - Ken Kurokawa
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, Japan.,Department of Informatics, National Institute of Genetics, Shizuoka, Japan
| | - Yuichi Hongoh
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, Japan.,School of Life Sciences and Technology, Tokyo Institute of Technology, Tokyo, Japan
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36
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Land H, Senger M, Berggren G, Stripp ST. Current State of [FeFe]-Hydrogenase Research: Biodiversity and Spectroscopic Investigations. ACS Catal 2020. [DOI: 10.1021/acscatal.0c01614] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Henrik Land
- Molecular Biomimetics, Department of Chemistry, Ångström Laboratory, Uppsala University, Uppsala 75120, Sweden
| | - Moritz Senger
- Physical Chemistry, Department of Chemistry, Ångström Laboratory, Uppsala University, Uppsala 75120, Sweden
- Bioinorganic Spectroscopy, Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Gustav Berggren
- Molecular Biomimetics, Department of Chemistry, Ångström Laboratory, Uppsala University, Uppsala 75120, Sweden
| | - Sven T. Stripp
- Bioinorganic Spectroscopy, Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
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The Role of Fnr Paralogs in Controlling Anaerobic Metabolism in the Diazotroph Paenibacillus polymyxa WLY78. Appl Environ Microbiol 2020; 86:AEM.03012-19. [PMID: 32198173 DOI: 10.1128/aem.03012-19] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Accepted: 02/28/2020] [Indexed: 11/20/2022] Open
Abstract
Fnr is a transcriptional regulator that controls the expression of a variety of genes in response to oxygen limitation in bacteria. Genome sequencing revealed four genes (fnr1, fnr3, fnr5, and fnr7) coding for Fnr proteins in Paenibacillus polymyxa WLY78. Fnr1 and Fnr3 showed more similarity to each other than to Fnr5 and Fnr7. Also, Fnr1 and Fnr3 exhibited high similarity with Bacillus cereus Fnr and Bacillus subtilis Fnr in sequence and structures. Both the aerobically purified His-tagged Fnr1 and His-tagged Fnr3 in Escherichia coli could bind to the specific DNA promoter. Deletion analysis showed that the four fnr genes, especially fnr1 and fnr3, have significant impacts on growth and nitrogenase activity. Single deletion of fnr1 or fnr3 led to a 50% reduction in nitrogenase activity, and double deletion of fnr1 and fnr3 resulted to a 90% reduction in activity. Genome-wide transcription analysis showed that Fnr1 and Fnr3 indirectly activated expression of nif (nitrogen fixation) genes and Fe transport genes under anaerobic conditions. Fnr1 and Fnr3 inhibited expression of the genes involved in the aerobic respiratory chain and activated expression of genes responsible for anaerobic electron acceptor genes.IMPORTANCE The members of the nitrogen-fixing Paenibacillus spp. have great potential to be used as a bacterial fertilizer in agriculture. However, the functions of the fnr gene(s) in nitrogen fixation and other metabolisms in Paenibacillus spp. are not known. Here, we found that in P. polymyxa WLY78, Fnr1 and Fnr3 were responsible for regulation of numerous genes in response to changes in oxygen levels, but Fnr5 and Fnr7 exhibited little effect. Fnr1 and Fnr3 indirectly or directly regulated many types of important metabolism, such as nitrogen fixation, Fe uptake, respiration, and electron transport. This study not only reveals the function of the fnr genes of P. polymyxa WLY78 in nitrogen fixation and other metabolisms but also will provide insight into the evolution and regulatory mechanisms of fnr in Paenibacillus.
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38
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Kannchen D, Zabret J, Oworah-Nkruma R, Dyczmons-Nowaczyk N, Wiegand K, Löbbert P, Frank A, Nowaczyk MM, Rexroth S, Rögner M. Remodeling of photosynthetic electron transport in Synechocystis sp. PCC 6803 for future hydrogen production from water. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2020; 1861:148208. [PMID: 32339488 DOI: 10.1016/j.bbabio.2020.148208] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2019] [Revised: 03/16/2020] [Accepted: 04/14/2020] [Indexed: 02/06/2023]
Abstract
Photosynthetic microorganisms such as the cyanobacterium Synechocystis sp. PCC 6803 (Synechocystis) can be exploited for the light-driven synthesis of valuable compounds. Thermodynamically, it is most beneficial to branch-off photosynthetic electrons at ferredoxin (Fd), which provides electrons for a variety of fundamental metabolic pathways in the cell, with the ferredoxin-NADP+ Oxido-Reductase (FNR, PetH) being the main target. In order to re-direct electrons from Fd to another consumer, the high electron transport rate between Fd and FNR has to be reduced. Based on our previous in vitro experiments, corresponding FNR-mutants at position FNR_K190 (Wiegand, K., et al.: "Rational redesign of the ferredoxin-NADP-oxido-reductase/ferredoxin-interaction for photosynthesis-dependent H2-production". Biochim Biophys Acta, 2018) have been generated in Synechocystis cells to study their impact on the cellular metabolism and their potential for a future hydrogen-producing design cell. Out of two promising candidates, mutation FNR_K190D proved to be lethal due to oxidative stress, while FNR_K190A was successfully generated and characterized: The light induced NADPH formation is clearly impaired in this mutant and it shows also major metabolic adaptations like a higher glucose metabolism as evidenced by quantitative mass spectrometric analysis. These results indicate a high potential for the future use of photosynthetic electrons in engineered design cells - for instance for hydrogen production. They also show substantial differences of interacting proteins in an in vitro environment vs. physiological conditions in whole cells.
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Affiliation(s)
- Daniela Kannchen
- Plant Biochemistry, Faculty of Biology and Biotechnology, Ruhr-University Bochum, 44780 Bochum, Germany
| | - Jure Zabret
- Plant Biochemistry, Faculty of Biology and Biotechnology, Ruhr-University Bochum, 44780 Bochum, Germany
| | - Regina Oworah-Nkruma
- Plant Biochemistry, Faculty of Biology and Biotechnology, Ruhr-University Bochum, 44780 Bochum, Germany
| | - Nina Dyczmons-Nowaczyk
- Plant Biochemistry, Faculty of Biology and Biotechnology, Ruhr-University Bochum, 44780 Bochum, Germany
| | - Katrin Wiegand
- Plant Biochemistry, Faculty of Biology and Biotechnology, Ruhr-University Bochum, 44780 Bochum, Germany
| | - Pia Löbbert
- Plant Biochemistry, Faculty of Biology and Biotechnology, Ruhr-University Bochum, 44780 Bochum, Germany
| | - Anna Frank
- Plant Biochemistry, Faculty of Biology and Biotechnology, Ruhr-University Bochum, 44780 Bochum, Germany
| | - Marc Michael Nowaczyk
- Plant Biochemistry, Faculty of Biology and Biotechnology, Ruhr-University Bochum, 44780 Bochum, Germany
| | - Sascha Rexroth
- Plant Biochemistry, Faculty of Biology and Biotechnology, Ruhr-University Bochum, 44780 Bochum, Germany
| | - Matthias Rögner
- Plant Biochemistry, Faculty of Biology and Biotechnology, Ruhr-University Bochum, 44780 Bochum, Germany.
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Mészáros LS, Ceccaldi P, Lorenzi M, Redman HJ, Pfitzner E, Heberle J, Senger M, Stripp ST, Berggren G. Spectroscopic investigations under whole-cell conditions provide new insight into the metal hydride chemistry of [FeFe]-hydrogenase. Chem Sci 2020; 11:4608-4617. [PMID: 34122916 PMCID: PMC8159234 DOI: 10.1039/d0sc00512f] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Hydrogenases are among the fastest H2 evolving catalysts known to date and have been extensively studied under in vitro conditions. Here, we report the first mechanistic investigation of an [FeFe]-hydrogenase under whole-cell conditions. Functional [FeFe]-hydrogenase from the green alga Chlamydomonas reinhardtii is generated in genetically modified Escherichia coli cells by addition of a synthetic cofactor to the growth medium. The assembly and reactivity of the resulting semi-synthetic enzyme was monitored using whole-cell electron paramagnetic resonance and Fourier-transform Infrared difference spectroscopy as well as scattering scanning near-field optical microscopy. Through a combination of gas treatments, pH titrations, and isotope editing we were able to corroborate the formation of a number of proposed catalytic intermediates in living cells, supporting their physiological relevance. Moreover, a previously incompletely characterized catalytic intermediate is reported herein, attributed to the formation of a protonated metal hydride species.
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Affiliation(s)
- Lívia S Mészáros
- Molecular Biomimetics, Dept. of Chemistry - Ångström Laboratory, Uppsala University Lägerhyddsvägen 1 SE-75120 Uppsala Sweden
| | - Pierre Ceccaldi
- Molecular Biomimetics, Dept. of Chemistry - Ångström Laboratory, Uppsala University Lägerhyddsvägen 1 SE-75120 Uppsala Sweden
| | - Marco Lorenzi
- Molecular Biomimetics, Dept. of Chemistry - Ångström Laboratory, Uppsala University Lägerhyddsvägen 1 SE-75120 Uppsala Sweden
| | - Holly J Redman
- Molecular Biomimetics, Dept. of Chemistry - Ångström Laboratory, Uppsala University Lägerhyddsvägen 1 SE-75120 Uppsala Sweden
| | - Emanuel Pfitzner
- Institute of Experimental Physics, Experimental Molecular Biophysics, Freie Universität Berlin Arnimallee 14 Berlin DE-14195 Germany
| | - Joachim Heberle
- Institute of Experimental Physics, Experimental Molecular Biophysics, Freie Universität Berlin Arnimallee 14 Berlin DE-14195 Germany
| | - Moritz Senger
- Institute of Experimental Physics, Experimental Molecular Biophysics, Freie Universität Berlin Arnimallee 14 Berlin DE-14195 Germany
| | - Sven T Stripp
- Institute of Experimental Physics, Experimental Molecular Biophysics, Freie Universität Berlin Arnimallee 14 Berlin DE-14195 Germany
| | - Gustav Berggren
- Molecular Biomimetics, Dept. of Chemistry - Ångström Laboratory, Uppsala University Lägerhyddsvägen 1 SE-75120 Uppsala Sweden
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40
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Swartz J. Opportunities toward hydrogen production biotechnologies. Curr Opin Biotechnol 2020; 62:248-255. [PMID: 32278260 DOI: 10.1016/j.copbio.2020.03.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 03/09/2020] [Accepted: 03/10/2020] [Indexed: 01/08/2023]
Abstract
Hydrogen is already a major commodity and process intermediate for fertilizer production, petroleum processing, and chemical synthesis. It also offers unrealized potential for energy storage. While biological production offers an expandable and sustainable source, enthusiasm has been dampened by slow research progress. Also, the very low cost of natural gas (the major current hydrogen source) imposes severe economic challenges. This discussion describes process, metabolic, and protein engineering opportunities toward cost-effective biohydrogen production. Recent progress in hydrogenase engineering and photosynthetic bacterial research now suggests a favorable risk versus reward opportunity. Although the risks are still significant, successful technologies would provide important components in an integrated energy portfolio that enables global sustainability.
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Affiliation(s)
- James Swartz
- Dept. of Chemical Engineering, Dept. of Bioengineering Stanford University, United States.
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41
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Ben-Zvi O, Dafni E, Feldman Y, Yacoby I. Re-routing photosynthetic energy for continuous hydrogen production in vivo. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:266. [PMID: 31737095 PMCID: PMC6844042 DOI: 10.1186/s13068-019-1608-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2019] [Accepted: 11/04/2019] [Indexed: 05/09/2023]
Abstract
BACKGROUND Hydrogen is considered a promising energy vector that can be produced from sustainable resources such as sunlight and water. In green algae, such as Chlamydomonas reinhardtii, photoproduction of hydrogen is catalyzed by the enzyme [FeFe]-hydrogenase (HydA). Although highly efficient, this process is transitory and thought to serve as a release valve for excess reducing power. Up to date, prolonged production of hydrogen was achieved by the deprivation of either nutrients or light, thus, hindering the full potential of photosynthetic hydrogen production. Previously we showed that the enzyme superoxide dismutase (SOD) can enhance HydA activity in vitro, specifically when tied together to a fusion protein. RESULTS In this work, we explored the in vivo hydrogen production phenotype of HydA-SOD fusion. We found a sustained hydrogen production, which is dependent on linear electron flow, although other pathways feed it as well. In addition, other characteristics such as slower growth and oxygen production were also observed in Hyd-SOD-expressing algae. CONCLUSIONS The Hyd-SOD fusion manages to outcompete the Calvin-Benson cycle, allowing sustained hydrogen production for up to 14 days in non-limiting conditions.
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Affiliation(s)
- Oren Ben-Zvi
- School of Plant Sciences and Food Security, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, Tel Aviv, 69978 Israel
| | - Eyal Dafni
- School of Plant Sciences and Food Security, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, Tel Aviv, 69978 Israel
| | - Yael Feldman
- School of Plant Sciences and Food Security, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, Tel Aviv, 69978 Israel
| | - Iftach Yacoby
- School of Plant Sciences and Food Security, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, Tel Aviv, 69978 Israel
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42
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Multilayered horizontal operon transfers from bacteria reconstruct a thiamine salvage pathway in yeasts. Proc Natl Acad Sci U S A 2019; 116:22219-22228. [PMID: 31611373 DOI: 10.1073/pnas.1909844116] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Horizontal acquisition of bacterial genes is presently recognized as an important contribution to the adaptation and evolution of eukaryotic genomes. However, the mechanisms underlying expression and consequent selection and fixation of the prokaryotic genes in the new eukaryotic setting are largely unknown. Here we show that genes composing the pathway for the synthesis of the essential vitamin B1 (thiamine) were lost in an ancestor of a yeast lineage, the Wickerhamiella/Starmerella (W/S) clade, known to harbor an unusually large number of genes of alien origin. The thiamine pathway was subsequently reassembled, at least twice, by multiple HGT events from different bacterial donors involving both single genes and entire operons. In the W/S-clade species Starmerella bombicola we obtained direct genetic evidence that all bacterial genes of the thiamine pathway are functional. The reconstructed pathway is composed by yeast and bacterial genes operating coordinately to scavenge thiamine derivatives from the environment. The adaptation of the newly acquired operons to the eukaryotic setting involved a repertoire of mechanisms until now only sparsely documented, namely longer intergenic regions, post-horizontal gene transfer (HGT) gene fusions fostering coordinated expression, gene relocation, and possibly recombination generating mosaic genes. The results provide additional evidence that HGT occurred recurrently in this yeast lineage and was crucial for the reestablishment of lost functions and that similar mechanisms are used across a broad range of eukaryotic microbes to promote adaptation of prokaryotic genes to their new environment.
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H-cluster assembly intermediates built on HydF by the radical SAM enzymes HydE and HydG. J Biol Inorg Chem 2019; 24:783-792. [PMID: 31493152 DOI: 10.1007/s00775-019-01709-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 08/13/2019] [Indexed: 12/12/2022]
Abstract
[FeFe]-hydrogenase catalyzes the reversible reduction of protons to H2 at a complex metallocofactor site, the H-cluster. Biosynthesis of this active-site H-cluster requires three maturation enzymes: the radical S-adenosylmethionine enzymes HydE and HydG synthesize the nonprotein ligands, while the GTPase HydF provides a scaffold for assembly of the 2Fe subcluster of the H-cluster ([2Fe]H) prior to its transfer to hydrogenase. To delineate the assembly and delivery steps for the 2Fe precursor cluster coordinated to HydF ([2Fe]F), we have heterologously expressed HydF in the presence of HydE alone (HydFE) or HydG alone (HydFG), and characterized the resulting purified HydFE and HydFG using UV-visible, EPR, and FTIR spectroscopies and biochemical assays. The iron-sulfur clusters on HydF are modified by co-expression with HydE or HydG, as evidenced by the changes in the visible, EPR, and FTIR spectral features. Further, biochemical assays show that HydFE is capable of activating HydAΔEFG to a limited extent (~ 1% of WT) even though the normal source of CO and CN- ligands of [2Fe]H (HydG) was absent. Activation assays performed with HydFG, in contrast, exhibit no ability to mature HydAΔEFG. It appears that in the case of HydFE, trace diatomics from the cellular environment are incorporated into a [2Fe]F-like precursor on HydF in the absence of HydG. We conclude that the product of HydE, presumably the dithiomethylamine ligand of [2Fe]H, is absolutely essential to the activation process, while the diatomic products of HydG can be provided from alternate sources.
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44
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Abstract
The active site (H-cluster) of [FeFe]-hydrogenases is a blueprint for the design of a biologically inspired H2-producing catalyst. The maturation process describes the preassembly and uptake of the unique [2FeH] cluster into apo-hydrogenase, which is to date not fully understood. In this study, we targeted individual amino acids by site-directed mutagenesis in the [FeFe]-hydrogenase CpI of Clostridium pasteurianum to reveal the final steps of H-cluster maturation occurring within apo-hydrogenase. We identified putative key positions for cofactor uptake and the subsequent structural reorganization that stabilizes the [2FeH] cofactor in its functional coordination sphere. Our results suggest that functional integration of the negatively charged [2FeH] precursor requires the positive charges and individual structural features of the 2 basic residues of arginine 449 and lysine 358, which mark the entrance and terminus of the maturation channel, respectively. The results obtained for 5 glycine-to-histidine exchange variants within a flexible loop region provide compelling evidence that the glycine residues function as hinge positions in the refolding process, which closes the secondary ligand sphere of the [2FeH] cofactor and the maturation channel. The conserved structural motifs investigated here shed light on the interplay between the secondary ligand sphere and catalytic cofactor.
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45
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Bai Y, Chen T, Happe T, Lu Y, Sawyer A. Iron-sulphur cluster biogenesis via the SUF pathway. Metallomics 2019; 10:1038-1052. [PMID: 30019043 DOI: 10.1039/c8mt00150b] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Iron-sulphur (Fe-S) clusters are versatile cofactors, which are essential for key metabolic processes in cells, such as respiration and photosynthesis, and which may have also played a crucial role in establishing life on Earth. They can be found in almost all living organisms, from unicellular prokaryotes and archaea to multicellular animals and plants, and exist in diverse forms. This review focuses on the most ancient Fe-S cluster assembly system, the sulphur utilization factor (SUF) mechanism, which is crucial in bacteria for cell survival under stress conditions such as oxidation and iron starvation, and which is also present in the chloroplasts of green microalgae and plants, where it is responsible for plastidial Fe-S protein maturation. We explain the SUF Fe-S cluster assembly process, the proteins involved, their regulation and provide evolutionary insights. We specifically focus on examples from Fe-S cluster synthesis in the model organisms Escherichia coli and Arabidopsis thaliana and discuss in an in vivo context the assembly of the [FeFe]-hydrogenase H-cluster from Chlamydomonas reinhardtii.
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Affiliation(s)
- Y Bai
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China.
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46
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Bridwell-Rabb J, Grell TAJ, Drennan CL. A Rich Man, Poor Man Story of S-Adenosylmethionine and Cobalamin Revisited. Annu Rev Biochem 2019; 87:555-584. [PMID: 29925255 DOI: 10.1146/annurev-biochem-062917-012500] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
S-adenosylmethionine (AdoMet) has been referred to as both "a poor man's adenosylcobalamin (AdoCbl)" and "a rich man's AdoCbl," but today, with the ever-increasing number of functions attributed to each cofactor, both appear equally rich and surprising. The recent characterization of an organometallic species in an AdoMet radical enzyme suggests that the line that differentiates them in nature will be constantly challenged. Here, we compare and contrast AdoMet and cobalamin (Cbl) and consider why Cbl-dependent AdoMet radical enzymes require two cofactors that are so similar in their reactivity. We further carry out structural comparisons employing the recently determined crystal structure of oxetanocin-A biosynthetic enzyme OxsB, the first three-dimensional structural data on a Cbl-dependent AdoMet radical enzyme. We find that the structural motifs responsible for housing the AdoMet radical machinery are largely conserved, whereas the motifs responsible for binding additional cofactors are much more varied.
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Affiliation(s)
- Jennifer Bridwell-Rabb
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA; , .,Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.,Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.,Present address: Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Tsehai A J Grell
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Catherine L Drennan
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA; , .,Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.,Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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47
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Németh B, Esmieu C, Redman HJ, Berggren G. Monitoring H-cluster assembly using a semi-synthetic HydF protein. Dalton Trans 2019; 48:5978-5986. [PMID: 30632592 PMCID: PMC6509880 DOI: 10.1039/c8dt04294b] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Accepted: 12/21/2018] [Indexed: 11/21/2022]
Abstract
The [FeFe] hydrogenase enzyme interconverts protons and molecular hydrogen with remarkable efficiency. The reaction is catalysed by a unique metallo-cofactor denoted as the H-cluster containing an organometallic dinuclear Fe component, the [2Fe] subsite. The HydF protein delivers a precursor of the [2Fe] subsite to the apo-[FeFe] hydrogenase, thus completing the H-cluster and activating the enzyme. Herein we generate a semi-synthetic form of HydF by loading it with a synthetic low valent dinuclear Fe complex. We show that this semi-synthetic protein is practically indistinguishable from the native protein, and utilize this form of HydF to explore the mechanism of H-cluster assembly. More specifically, we show that transfer of the precatalyst from HydF to the hydrogenase enzyme results in the release of CO, underscoring that the pre-catalyst is a four CO species when bound to HydF. Moreover, we propose that an electron transfer reaction occurs during H-cluster assembly, resulting in an oxidation of the [2Fe] subsite with concomitant reduction of the [4Fe4S] cluster present on the HydF protein.
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Affiliation(s)
- Brigitta Németh
- Molecular Biomimetics
, Department of Chemistry – Ångström Laboratory
, Uppsala University
,
75120 Uppsala
, Sweden
.
| | - Charlène Esmieu
- Molecular Biomimetics
, Department of Chemistry – Ångström Laboratory
, Uppsala University
,
75120 Uppsala
, Sweden
.
| | - Holly J. Redman
- Molecular Biomimetics
, Department of Chemistry – Ångström Laboratory
, Uppsala University
,
75120 Uppsala
, Sweden
.
| | - Gustav Berggren
- Molecular Biomimetics
, Department of Chemistry – Ångström Laboratory
, Uppsala University
,
75120 Uppsala
, Sweden
.
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48
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Transcriptional Regulation of the Equol Biosynthesis Gene Cluster in Adlercreutzia equolifaciens DSM19450 T. Nutrients 2019; 11:nu11050993. [PMID: 31052328 PMCID: PMC6566806 DOI: 10.3390/nu11050993] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 04/26/2019] [Accepted: 04/30/2019] [Indexed: 02/06/2023] Open
Abstract
Given the emerging evidence of equol’s benefit to human health, understanding its synthesis and regulation in equol-producing bacteria is of paramount importance. Adlercreutzia equolifaciens DSM19450T is a human intestinal bacterium—for which the whole genome sequence is publicly available—that produces equol from the daidzein isoflavone. In the present work, daidzein (between 50 to 200 μM) was completely metabolized by cultures of A. equolifaciens DSM19450T after 10 h of incubation. However, only about one third of the added isoflavone was transformed into dihydrodaidzein and then into equol. Transcriptional analysis of the ORFs and intergenic regions of the bacterium’s equol gene cluster was therefore undertaken using RT-PCR and RT-qPCR techniques with the aim of identifying the genetic elements of equol biosynthesis and its regulation mechanisms. Compared to controls cultured without daidzein, the expression of all 13 contiguous genes in the equol cluster was enhanced in the presence of the isoflavone. Depending on the gene and the amount of daidzein in the medium, overexpression varied from 0.5- to about 4-log10 units. Four expression patterns of transcription were identified involving genes within the cluster. The genes dzr, ddr and tdr, which code for daidzein reductase, dihydrodaidzein reductase and tetrahydrodaidzein reductase respectively, and which have been shown involved in equol biosynthesis, were among the most strongly expressed genes in the cluster. These expression patterns correlated with the location of four putative ρ-independent terminator sequences in the cluster. All the intergenic regions were amplified by RT-PCR, indicating the operon to be transcribed as a single RNA molecule. These findings provide new knowledge on the metabolic transformation of daidzein into equol by A. equolifaciens DSM19450T, which might help in efforts to increase the endogenous formation of this compound and/or its biotechnological production.
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49
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Liu Y, Mohammadi M, Vashisth H. Diffusion network of CO in FeFe-Hydrogenase. J Chem Phys 2018; 149:204108. [PMID: 30501239 DOI: 10.1063/1.5054877] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
FeFe-hydrogenase is an efficient enzyme to produce H2 under optimal conditions. However, the activity of this enzyme is highly sensitive to the presence of inhibitory gases CO and O2 that cause irreversible damage to the active site. Therefore, a detailed knowledge of the diffusion pathways of these inhibitory gases is necessary to develop strategies for designing novel enzymes that are tolerant to these gases. In this work, we studied the diffusion pathways of CO in the CpI FeFe-hydrogenase from Clostridium pasteurianum. Specifically, we used several enhanced sampling and free-energy simulation methods to reconstruct a three-dimensional free-energy surface for CO diffusion which revealed 45 free-energy minima forming an interconnected network of pathways. We discovered multiple pathways of minimal free-energy as diffusion portals for CO and found that previously suggested hydrophobic pathways are not thermodynamically favorable for CO diffusion. We also observed that the global minimum in the free-energy surface is located in the vicinity of the active-site metal cluster, the H-cluster, which suggests a high-affinity for CO near the active site. Among 19 potential residues that we propose as candidates for future mutagenesis studies, 11 residues are shared with residues that have been previously proposed to increase the tolerance of this enzyme for O2. We hypothesize that these shared candidate residues are potentially useful for designing new variants of this enzyme that are tolerant to both inhibitory gases.
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Affiliation(s)
- Yong Liu
- Department of Chemical Engineering, University of New Hampshire, 33 Academic Way, Durham, New Hampshire 03824, USA
| | - Mohammadjavad Mohammadi
- Department of Chemical Engineering, University of New Hampshire, 33 Academic Way, Durham, New Hampshire 03824, USA
| | - Harish Vashisth
- Department of Chemical Engineering, University of New Hampshire, 33 Academic Way, Durham, New Hampshire 03824, USA
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50
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Ghirardi M, Subramanian V, Wecker M, Smolinski S, Antonio R, Xiong W, Gonzalez-Ballester D, Dubini A. Survey of the anaerobic metabolism of various laboratory wild-type Chlamydomonas reinhardtii strains. ALGAL RES 2018. [DOI: 10.1016/j.algal.2018.05.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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