1
|
Understanding 2D-IR Spectra of Hydrogenases: A Descriptive and Predictive Computational Study. Catalysts 2022. [DOI: 10.3390/catal12090988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
[NiFe] hydrogenases are metalloenzymes that catalyze the reversible cleavage of dihydrogen (), a clean future fuel. Understanding the mechanism of these biocatalysts requires spectroscopic techniques that yield insights into the structure and dynamics of the [NiFe] active site. Due to the presence of CO and ligands at this cofactor, infrared (IR) spectroscopy represents an ideal technique for studying these aspects, but molecular information from linear IR absorption experiments is limited. More detailed insights can be obtained from ultrafast nonlinear IR techniques like IRpump−IRprobe and two-dimensional (2D-)IR spectroscopy. However, fully exploiting these advanced techniques requires an in-depth understanding of experimental observables and the encoded molecular information. To address this challenge, we present a descriptive and predictive computational approach for the simulation and analysis of static 2D-IR spectra of [NiFe] hydrogenases and similar organometallic systems. Accurate reproduction of experimental spectra from a first-coordination-sphere model suggests a decisive role of the [NiFe] core in shaping the enzymatic potential energy surface. We also reveal spectrally encoded molecular information that is not accessible by experiments, thereby helping to understand the catalytic role of the diatomic ligands, structural differences between [NiFe] intermediates, and possible energy transfer mechanisms. Our studies demonstrate the feasibility and benefits of computational spectroscopy in the 2D-IR investigation of hydrogenases, thereby further strengthening the potential of this nonlinear IR technique as a powerful research tool for the investigation of complex bioinorganic molecules.
Collapse
|
2
|
Kucera J, Lochman J, Bouchal P, Pakostova E, Mikulasek K, Hedrich S, Janiczek O, Mandl M, Johnson DB. A Model of Aerobic and Anaerobic Metabolism of Hydrogen in the Extremophile Acidithiobacillus ferrooxidans. Front Microbiol 2020; 11:610836. [PMID: 33329503 PMCID: PMC7735108 DOI: 10.3389/fmicb.2020.610836] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Accepted: 11/04/2020] [Indexed: 12/12/2022] Open
Abstract
Hydrogen can serve as an electron donor for chemolithotrophic acidophiles, especially in the deep terrestrial subsurface and geothermal ecosystems. Nevertheless, the current knowledge of hydrogen utilization by mesophilic acidophiles is minimal. A multi-omics analysis was applied on Acidithiobacillus ferrooxidans growing on hydrogen, and a respiratory model was proposed. In the model, [NiFe] hydrogenases oxidize hydrogen to two protons and two electrons. The electrons are used to reduce membrane-soluble ubiquinone to ubiquinol. Genetically associated iron-sulfur proteins mediate electron relay from the hydrogenases to the ubiquinone pool. Under aerobic conditions, reduced ubiquinol transfers electrons to either cytochrome aa 3 oxidase via cytochrome bc 1 complex and cytochrome c 4 or the alternate directly to cytochrome bd oxidase, resulting in proton efflux and reduction of oxygen. Under anaerobic conditions, reduced ubiquinol transfers electrons to outer membrane cytochrome c (ferrireductase) via cytochrome bc 1 complex and a cascade of electron transporters (cytochrome c 4, cytochrome c 552, rusticyanin, and high potential iron-sulfur protein), resulting in proton efflux and reduction of ferric iron. The proton gradient generated by hydrogen oxidation maintains the membrane potential and allows the generation of ATP and NADH. These results further clarify the role of extremophiles in biogeochemical processes and their impact on the composition of the deep terrestrial subsurface.
Collapse
Affiliation(s)
- Jiri Kucera
- Department of Biochemistry, Faculty of Science, Masaryk University, Brno, Czechia
| | - Jan Lochman
- Department of Biochemistry, Faculty of Science, Masaryk University, Brno, Czechia
| | - Pavel Bouchal
- Department of Biochemistry, Faculty of Science, Masaryk University, Brno, Czechia
| | - Eva Pakostova
- School of Biological Sciences, College of Natural Sciences, Bangor University, Bangor, United Kingdom
| | - Kamil Mikulasek
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Brno, Czechia
| | - Sabrina Hedrich
- Institute of Biosciences, Technische Universität (TU) Bergakademie Freiberg, Freiberg, Germany
| | - Oldrich Janiczek
- Department of Biochemistry, Faculty of Science, Masaryk University, Brno, Czechia
| | - Martin Mandl
- Department of Biochemistry, Faculty of Science, Masaryk University, Brno, Czechia
| | - D Barrie Johnson
- School of Biological Sciences, College of Natural Sciences, Bangor University, Bangor, United Kingdom
| |
Collapse
|
3
|
Gao XY, Fu CA, Hao L, Gu XF, Wang R, Lin JQ, Liu XM, Pang X, Zhang CJ, Lin JQ, Chen LX. The substrate-dependent regulatory effects of the AfeI/R system in Acidithiobacillus ferrooxidans reveals the novel regulation strategy of quorum sensing in acidophiles. Environ Microbiol 2020; 23:757-773. [PMID: 32656931 PMCID: PMC7984328 DOI: 10.1111/1462-2920.15163] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 07/05/2020] [Indexed: 12/22/2022]
Abstract
A LuxI/R‐like quorum sensing (QS) system (AfeI/R) has been reported in the acidophilic and chemoautotrophic Acidithiobacillus spp. However, the function of AfeI/R remains unclear because of the difficulties in the genetic manipulation of these bacteria. Here, we constructed different afeI mutants of the sulfur‐ and iron‐oxidizer A. ferrooxidans, identified the N‐acyl homoserine lactones (acyl‐HSLs) synthesized by AfeI, and determined the regulatory effects of AfeI/R on genes expression, extracellular polymeric substance synthesis, energy metabolism, cell growth and population density of A. ferrooxidans in different energy substrates. Acyl‐HSLs‐mediated distinct regulation strategies were employed to influence bacterial metabolism and cell growth of A. ferrooxidans cultivated in either sulfur or ferrous iron. Based on these findings, an energy‐substrate‐dependent regulation mode of AfeI/R in A. ferrooxidans was illuminated that AfeI/R could produce different types of acyl‐HSLs and employ specific acyl‐HSLs to regulate specific genes in response to different energy substrates. The discovery of the AfeI/R‐mediated substrate‐dependent regulatory mode expands our knowledge on the function of QS system in the chemoautotrophic sulfur‐ and ferrous iron‐oxidizing bacteria, and provides new insights in understanding energy metabolism modulation, population control, bacteria‐driven bioleaching process, and the coevolution between the acidophiles and their acidic habitats.
Collapse
Affiliation(s)
- Xue-Yan Gao
- State Key Laboratory of Microbial Technology, Shandong University, No. 72 Binhai Road, Qingdao, 266237, China
| | - Chang-Ai Fu
- State Key Laboratory of Microbial Technology, Shandong University, No. 72 Binhai Road, Qingdao, 266237, China
| | - Likai Hao
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, No. 99 Lincheng West Road, Guiyang, 550081, China.,CAS Center for Excellence in Quaternary Science and Global Change, Xi'an, 710061, China
| | - Xiu-Feng Gu
- State Key Laboratory of Microbial Technology, Shandong University, No. 72 Binhai Road, Qingdao, 266237, China
| | - Rui Wang
- State Key Laboratory of Microbial Technology, Shandong University, No. 72 Binhai Road, Qingdao, 266237, China
| | - Jian-Qiang Lin
- State Key Laboratory of Microbial Technology, Shandong University, No. 72 Binhai Road, Qingdao, 266237, China
| | - Xiang-Mei Liu
- State Key Laboratory of Microbial Technology, Shandong University, No. 72 Binhai Road, Qingdao, 266237, China
| | - Xin Pang
- State Key Laboratory of Microbial Technology, Shandong University, No. 72 Binhai Road, Qingdao, 266237, China
| | - Cheng-Jia Zhang
- State Key Laboratory of Microbial Technology, Shandong University, No. 72 Binhai Road, Qingdao, 266237, China
| | - Jian-Qun Lin
- State Key Laboratory of Microbial Technology, Shandong University, No. 72 Binhai Road, Qingdao, 266237, China
| | - Lin-Xu Chen
- State Key Laboratory of Microbial Technology, Shandong University, No. 72 Binhai Road, Qingdao, 266237, China
| |
Collapse
|
4
|
Islam ZF, Cordero PRF, Greening C. Putative Iron-Sulfur Proteins Are Required for Hydrogen Consumption and Enhance Survival of Mycobacteria. Front Microbiol 2019; 10:2749. [PMID: 31824474 PMCID: PMC6883350 DOI: 10.3389/fmicb.2019.02749] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Accepted: 11/12/2019] [Indexed: 01/01/2023] Open
Abstract
Aerobic soil bacteria persist by scavenging molecular hydrogen (H2) from the atmosphere. This key process is the primary sink in the biogeochemical hydrogen cycle and supports the productivity of oligotrophic ecosystems. In Mycobacterium smegmatis, atmospheric H2 oxidation is catalyzed by two phylogenetically distinct [NiFe]-hydrogenases, Huc (group 2a) and Hhy (group 1h). However, it is currently unresolved how these enzymes transfer electrons derived from H2 oxidation into the aerobic respiratory chain. In this work, we used genetic approaches to confirm that two putative iron-sulfur cluster proteins encoded on the hydrogenase structural operons, HucE and HhyE, are required for H2 consumption in M. smegmatis. Sequence analysis show that these proteins, while homologous, fall into distinct phylogenetic clades and have distinct metal-binding motifs. H2 oxidation was reduced when the genes encoding these proteins were deleted individually and was eliminated when they were deleted in combination. In turn, the growth yield and long-term survival of these deletion strains was modestly but significantly reduced compared to the parent strain. In both biochemical and phenotypic assays, the mutant strains lacking the putative iron-sulfur proteins phenocopied those of hydrogenase structural subunit mutants. We hypothesize that these proteins mediate electron transfer between the catalytic subunits of the hydrogenases and the menaquinone pool of the M. smegmatis respiratory chain; however, other roles (e.g., in maturation) are also plausible and further work is required to resolve their role. The conserved nature of these proteins within most Hhy- or Huc-encoding organisms suggests that these proteins are important determinants of atmospheric H2 oxidation.
Collapse
Affiliation(s)
| | | | - Chris Greening
- School of Biological Sciences, Monash University, Clayton, VIC, Australia
| |
Collapse
|
5
|
Infrared Characterization of the Bidirectional Oxygen-Sensitive [NiFe]-Hydrogenase from E. coli. Catalysts 2018. [DOI: 10.3390/catal8110530] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
[NiFe]-hydrogenases are gas-processing metalloenzymes that catalyze the conversion of dihydrogen (H2) to protons and electrons in a broad range of microorganisms. Within the framework of green chemistry, the molecular proceedings of biological hydrogen turnover inspired the design of novel catalytic compounds for H2 generation. The bidirectional “O2-sensitive” [NiFe]-hydrogenase from Escherichia coli HYD-2 has recently been crystallized; however, a systematic infrared characterization in the presence of natural reactants is not available yet. In this study, we analyze HYD-2 from E. coli by in situ attenuated total reflection Fourier-transform infrared spectroscopy (ATR FTIR) under quantitative gas control. We provide an experimental assignment of all catalytically relevant redox intermediates alongside the O2- and CO-inhibited cofactor species. Furthermore, the reactivity and mutual competition between H2, O2, and CO was probed in real time, which lays the foundation for a comparison with other enzymes, e.g., “O2-tolerant” [NiFe]-hydrogenases. Surprisingly, only Ni-B was observed in the presence of O2 with no indications for the “unready” Ni-A state. The presented work proves the capabilities of in situ ATR FTIR spectroscopy as an efficient and powerful technique for the analysis of biological macromolecules and enzymatic small molecule catalysis.
Collapse
|
6
|
Petrenko A, Stein M. Distal [FeS]-Cluster Coordination in [NiFe]-Hydrogenase Facilitates Intermolecular Electron Transfer. Int J Mol Sci 2017; 18:ijms18010100. [PMID: 28067774 PMCID: PMC5297734 DOI: 10.3390/ijms18010100] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Revised: 12/28/2016] [Accepted: 12/30/2016] [Indexed: 11/29/2022] Open
Abstract
Biohydrogen is a versatile energy carrier for the generation of electric energy from renewable sources. Hydrogenases can be used in enzymatic fuel cells to oxidize dihydrogen. The rate of electron transfer (ET) at the anodic side between the [NiFe]-hydrogenase enzyme distal iron–sulfur cluster and the electrode surface can be described by the Marcus equation. All parameters for the Marcus equation are accessible from Density Functional Theory (DFT) calculations. The distal cubane FeS-cluster has a three-cysteine and one-histidine coordination [Fe4S4](His)(Cys)3 first ligation sphere. The reorganization energy (inner- and outer-sphere) is almost unchanged upon a histidine-to-cysteine substitution. Differences in rates of electron transfer between the wild-type enzyme and an all-cysteine mutant can be rationalized by a diminished electronic coupling between the donor and acceptor molecules in the [Fe4S4](Cys)4 case. The fast and efficient electron transfer from the distal iron–sulfur cluster is realized by a fine-tuned protein environment, which facilitates the flow of electrons. This study enables the design and control of electron transfer rates and pathways by protein engineering.
Collapse
Affiliation(s)
- Alexander Petrenko
- Max Planck Institute for Dynamics of Complex Technical Systems, Molecular Simulations and Design Group, Sandtorstrasse 1, 39106 Magdeburg, Germany.
| | - Matthias Stein
- Max Planck Institute for Dynamics of Complex Technical Systems, Molecular Simulations and Design Group, Sandtorstrasse 1, 39106 Magdeburg, Germany.
| |
Collapse
|
7
|
Zhang X, Liu X, Liang Y, Fan F, Zhang X, Yin H. Metabolic diversity and adaptive mechanisms of iron- and/or sulfur-oxidizing autotrophic acidophiles in extremely acidic environments. ENVIRONMENTAL MICROBIOLOGY REPORTS 2016; 8:738-751. [PMID: 27337207 DOI: 10.1111/1758-2229.12435] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Accepted: 05/30/2016] [Indexed: 06/06/2023]
Abstract
Many studies have investigated the mechanisms underlying the survival and growth of certain organisms in extremely acidic environments known to be harmful to most prokaryotes and eukaryotes. Acidithiobacillus and Leptospirillum spp. are dominant bioleaching bacteria widely used in bioleaching systems, which are characterized by extremely acidic environments. To survive and grow in such settings, these acidophiles utilize shared molecular mechanisms that allow life in extreme conditions. In this review, we have summarized the results of published genomic analyses, which underscore the ability of iron- and/or sulfur-oxidizing autotrophic acidophiles belonging to the genera Acidithiobacillus and Leptospirillum to adapt to acidic environmental conditions. Several lines of evidence point at the metabolic diversity and multiplicity of pathways involved in the survival of these organisms. The ability to thrive in adverse environments requires versatile activation of structural and functional adaptive responses, including bacterial adhesion, motility, and resistance to heavy metals. We have highlighted recent developments centered on the key survival mechanisms employed by dominant extremophiles, and have laid the foundation for future studies focused on the ability of acidophiles to thrive in extremely acidic environments.
Collapse
Affiliation(s)
- Xian Zhang
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
| | - Xueduan Liu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
| | - Yili Liang
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
| | - Fenliang Fan
- Key Laboratory of Plant Nutrition and Fertilizer, Beijing, China
| | - Xiaoxia Zhang
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture, Beijing, China
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Huaqun Yin
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
| |
Collapse
|
8
|
Qiu S, Azofra LM, MacFarlane DR, Sun C. Unraveling the Role of Ligands in the Hydrogen Evolution Mechanism Catalyzed by [NiFe] Hydrogenases. ACS Catal 2016. [DOI: 10.1021/acscatal.6b01359] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Siyao Qiu
- School
of Chemistry, Faculty of Science, Monash University, Clayton, Victoria 3800, Australia
| | - Luis Miguel Azofra
- School
of Chemistry, Faculty of Science, Monash University, Clayton, Victoria 3800, Australia
- ARC
Centre of Excellence for Electromaterials Science (ACES), School of
Chemistry, Faculty of Science, Monash University, Clayton, Victoria 3800, Australia
| | - Douglas R. MacFarlane
- School
of Chemistry, Faculty of Science, Monash University, Clayton, Victoria 3800, Australia
- ARC
Centre of Excellence for Electromaterials Science (ACES), School of
Chemistry, Faculty of Science, Monash University, Clayton, Victoria 3800, Australia
| | - Chenghua Sun
- School
of Chemistry, Faculty of Science, Monash University, Clayton, Victoria 3800, Australia
- ARC
Centre of Excellence for Electromaterials Science (ACES), School of
Chemistry, Faculty of Science, Monash University, Clayton, Victoria 3800, Australia
| |
Collapse
|
9
|
Raleiras P, Hammarström L, Lindblad P, Styring S, Magnuson A. Photoinduced reduction of the medial FeS center in the hydrogenase small subunit HupS from Nostoc punctiforme. J Inorg Biochem 2015; 148:57-61. [DOI: 10.1016/j.jinorgbio.2015.03.018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Revised: 03/22/2015] [Accepted: 03/24/2015] [Indexed: 12/21/2022]
|
10
|
Affiliation(s)
- Wolfgang Lubitz
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Hideaki Ogata
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Olaf Rüdiger
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Edward Reijerse
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, 45470 Mülheim an der Ruhr, Germany
| |
Collapse
|
11
|
Raleiras P, Kellers P, Lindblad P, Styring S, Magnuson A. Isolation and characterization of the small subunit of the uptake hydrogenase from the cyanobacterium Nostoc punctiforme. J Biol Chem 2013; 288:18345-52. [PMID: 23649626 DOI: 10.1074/jbc.m113.468587] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In nitrogen-fixing cyanobacteria, hydrogen evolution is associated with hydrogenases and nitrogenase, making these enzymes interesting targets for genetic engineering aimed at increased hydrogen production. Nostoc punctiforme ATCC 29133 is a filamentous cyanobacterium that expresses the uptake hydrogenase HupSL in heterocysts under nitrogen-fixing conditions. Little is known about the structural and biophysical properties of HupSL. The small subunit, HupS, has been postulated to contain three iron-sulfur clusters, but the details regarding their nature have been unclear due to unusual cluster binding motifs in the amino acid sequence. We now report the cloning and heterologous expression of Nostoc punctiforme HupS as a fusion protein, f-HupS. We have characterized the anaerobically purified protein by UV-visible and EPR spectroscopies. Our results show that f-HupS contains three iron-sulfur clusters. UV-visible absorption of f-HupS has bands ∼340 and 420 nm, typical for iron-sulfur clusters. The EPR spectrum of the oxidized f-HupS shows a narrow g = 2.023 resonance, characteristic of a low-spin (S = ½) [3Fe-4S] cluster. The reduced f-HupS presents complex EPR spectra with overlapping resonances centered on g = 1.94, g = 1.91, and g = 1.88, typical of low-spin (S = ½) [4Fe-4S] clusters. Analysis of the spectroscopic data allowed us to distinguish between two species attributable to two distinct [4Fe-4S] clusters, in addition to the [3Fe-4S] cluster. This indicates that f-HupS binds [4Fe-4S] clusters despite the presence of unusual coordinating amino acids. Furthermore, our expression and purification of what seems to be an intact HupS protein allows future studies on the significance of ligand nature on redox properties of the iron-sulfur clusters of HupS.
Collapse
Affiliation(s)
- Patrícia Raleiras
- Department of Chemistry, Ångström Laboratory, Uppsala University, SE-75120 Uppsala, Sweden
| | | | | | | | | |
Collapse
|
12
|
Kampa M, Pandelia ME, Lubitz W, van Gastel M, Neese F. A Metal–Metal Bond in the Light-Induced State of [NiFe] Hydrogenases with Relevance to Hydrogen Evolution. J Am Chem Soc 2013; 135:3915-25. [DOI: 10.1021/ja3115899] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Mario Kampa
- Max-Planck-Institut für Chemische Energiekonversion, Stiftstrasse 34-36, D-45470 Mülheim
an der Ruhr, Germany
| | - Maria-Eirini Pandelia
- Max-Planck-Institut für Chemische Energiekonversion, Stiftstrasse 34-36, D-45470 Mülheim
an der Ruhr, Germany
| | - Wolfgang Lubitz
- Max-Planck-Institut für Chemische Energiekonversion, Stiftstrasse 34-36, D-45470 Mülheim
an der Ruhr, Germany
| | - Maurice van Gastel
- Max-Planck-Institut für Chemische Energiekonversion, Stiftstrasse 34-36, D-45470 Mülheim
an der Ruhr, Germany
| | - Frank Neese
- Max-Planck-Institut für Chemische Energiekonversion, Stiftstrasse 34-36, D-45470 Mülheim
an der Ruhr, Germany
| |
Collapse
|
13
|
Anaerobic sulfur metabolism coupled to dissimilatory iron reduction in the extremophile Acidithiobacillus ferrooxidans. Appl Environ Microbiol 2013; 79:2172-81. [PMID: 23354702 DOI: 10.1128/aem.03057-12] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Gene transcription (microarrays) and protein levels (proteomics) were compared in cultures of the acidophilic chemolithotroph Acidithiobacillus ferrooxidans grown on elemental sulfur as the electron donor under aerobic and anaerobic conditions, using either molecular oxygen or ferric iron as the electron acceptor, respectively. No evidence supporting the role of either tetrathionate hydrolase or arsenic reductase in mediating the transfer of electrons to ferric iron (as suggested by previous studies) was obtained. In addition, no novel ferric iron reductase was identified. However, data suggested that sulfur was disproportionated under anaerobic conditions, forming hydrogen sulfide via sulfur reductase and sulfate via heterodisulfide reductase and ATP sulfurylase. Supporting physiological evidence for H2S production came from the observation that soluble Cu(2+) included in anaerobically incubated cultures was precipitated (seemingly as CuS). Since H(2)S reduces ferric iron to ferrous in acidic medium, its production under anaerobic conditions indicates that anaerobic iron reduction is mediated, at least in part, by an indirect mechanism. Evidence was obtained for an alternative model implicating the transfer of electrons from S(0) to Fe(3+) via a respiratory chain that includes a bc(1) complex and a cytochrome c. Central carbon pathways were upregulated under aerobic conditions, correlating with higher growth rates, while many Calvin-Benson-Bassham cycle components were upregulated during anaerobic growth, probably as a result of more limited access to carbon dioxide. These results are important for understanding the role of A. ferrooxidans in environmental biogeochemical metal cycling and in industrial bioleaching operations.
Collapse
|
14
|
Pandelia ME, Lubitz W, Nitschke W. Evolution and diversification of Group 1 [NiFe] hydrogenases. Is there a phylogenetic marker for O2-tolerance? BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2012; 1817:1565-75. [DOI: 10.1016/j.bbabio.2012.04.012] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2012] [Revised: 04/21/2012] [Accepted: 04/24/2012] [Indexed: 10/28/2022]
|
15
|
Germer F, Zebger I, Saggu M, Lendzian F, Schulz R, Appel J. Overexpression, isolation, and spectroscopic characterization of the bidirectional [NiFe] hydrogenase from Synechocystis sp. PCC 6803. J Biol Chem 2009; 284:36462-36472. [PMID: 19801638 DOI: 10.1074/jbc.m109.028795] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The bidirectional [NiFe] hydrogenase of the cyanobacterium Synechocystis sp. PCC 6803 was purified to apparent homogeneity by a single affinity chromatography step using a Synechocystis mutant with a Strep-tag II fused to the C terminus of HoxF. To increase the yield of purified enzyme and to test its overexpression capacity in Synechocystis the psbAII promoter was inserted upstream of the hoxE gene. In addition, the accessory genes (hypF, C, D, E, A, and B) from Nostoc sp. PCC 7120 were expressed under control of the psbAII promoter. The respective strains show higher hydrogenase activities compared with the wild type. For the first time a Fourier transform infrared (FTIR) spectroscopic characterization of a [NiFe] hydrogenase from an oxygenic phototroph is presented, revealing that two cyanides and one carbon monoxide coordinate the iron of the active site. At least four different redox states of the active site were detected during the reversible activation/inactivation. Although these states appear similar to those observed in standard [NiFe] hydrogenases, no paramagnetic nickel state could be detected in the fully oxidized and reduced forms. Electron paramagnetic resonance spectroscopy confirms the presence of several iron-sulfur clusters after reductive activation. One [4Fe4S](+) and at least one [2Fe2S](+) cluster could be identified. Catalytic amounts of NADH or NADPH are sufficient to activate the reaction of this enzyme with hydrogen.
Collapse
Affiliation(s)
- Frauke Germer
- Botanisches Institut, Universität Kiel, Am Botanischen Garten 1-9, D-24118 Kiel, Germany
| | - Ingo Zebger
- Max-Volmer-Laboratorium, Technische Universität Berlin, Strasse des 17, Juni 135, D-10623 Berlin, Germany
| | - Miguel Saggu
- Max-Volmer-Laboratorium, Technische Universität Berlin, Strasse des 17, Juni 135, D-10623 Berlin, Germany
| | - Friedhelm Lendzian
- Max-Volmer-Laboratorium, Technische Universität Berlin, Strasse des 17, Juni 135, D-10623 Berlin, Germany
| | - Rüdiger Schulz
- Botanisches Institut, Universität Kiel, Am Botanischen Garten 1-9, D-24118 Kiel, Germany
| | - Jens Appel
- School of Life Sciences, Arizona State University, Tempe, Arizona 85287.
| |
Collapse
|
16
|
Tard C, Pickett CJ. Structural and functional analogues of the active sites of the [Fe]-, [NiFe]-, and [FeFe]-hydrogenases. Chem Rev 2009; 109:2245-74. [PMID: 19438209 DOI: 10.1021/cr800542q] [Citation(s) in RCA: 1016] [Impact Index Per Article: 67.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Cédric Tard
- Laboratoire d'Electrochimie Moléculaire, Unité Mixte de Recherche Université-CNRS 7591, Université Paris Diderot, 75013 Paris, France
| | | |
Collapse
|
17
|
Probing intermediates in the activation cycle of [NiFe] hydrogenase by infrared spectroscopy: the Ni-SIr state and its light sensitivity. J Biol Inorg Chem 2009; 14:1227-41. [PMID: 19626348 PMCID: PMC2847147 DOI: 10.1007/s00775-009-0566-9] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2009] [Accepted: 06/26/2009] [Indexed: 11/08/2022]
Abstract
The [NiFe] hydrogenase from the sulphate-reducing bacterium Desulfovibrio vulgaris Miyazaki F is reversibly inhibited in the presence of molecular oxygen. A key intermediate in the reactivation process, Ni-SIr, provides the link between fully oxidized (Ni-A, Ni-B) and active (Ni-SIa, Ni-C and Ni-R) forms of hydrogenase. In this work Ni-SIr was found to be light-sensitive (T ≤ 110 K), similar to the active Ni-C and the CO-inhibited states. Transition to the final photoproduct state (Ni-SL) was shown to involve an additional transient light-induced state (Ni-SI1961). Rapid scan kinetic infrared measurements provided activation energies for the transition from Ni-SL to Ni-SIr in protonated as well as in deuterated samples. The inhibitor CO was found not to react with the active site of the Ni-SL state. The wavelength dependence of the Ni-SIr photoconversion was examined in the range between 410 and 680 nm. Light-induced effects were associated with a nickel-centred electronic transition, possibly involving a change in the spin state of nickel (Ni2+). In addition, at T ≤ 40 K the CN− stretching vibrations of Ni-SL were found to be dependent on the colour of the monochromatic light used to irradiate the species, suggesting a change in the interaction of the hydrogen-bonding network of the surrounding amino acids. A possible mechanism for the photochemical process, involving displacement of the oxygen-based ligand, is discussed.
Collapse
|
18
|
Saggu M, Zebger I, Ludwig M, Lenz O, Friedrich B, Hildebrandt P, Lendzian F. Spectroscopic insights into the oxygen-tolerant membrane-associated [NiFe] hydrogenase of Ralstonia eutropha H16. J Biol Chem 2009; 284:16264-16276. [PMID: 19304663 DOI: 10.1074/jbc.m805690200] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
This study provides the first spectroscopic characterization of the membrane-bound oxygen-tolerant [NiFe] hydrogenase (MBH) from Ralstonia eutropha H16 in its natural environment, the cytoplasmic membrane. The H2-converting MBH is composed of a large subunit, harboring the [NiFe] active site, and a small subunit, capable in coordinating one [3Fe4S] and two [4Fe4S] clusters. The hydrogenase dimer is electronically connected to a membrane-integral cytochrome b. EPR and Fourier transform infrared spectroscopy revealed a strong similarity of the MBH active site with known [NiFe] centers from strictly anaerobic hydrogenases. Most redox states characteristic for anaerobic [NiFe] hydrogenases were identified except for one remarkable difference. The formation of the oxygen-inhibited Niu-A state was never observed. Furthermore, EPR data showed the presence of an additional paramagnetic center at high redox potential (+290 mV), which couples magnetically to the [3Fe4S] center and indicates a structural and/or redox modification at or near the proximal [4Fe4S] cluster. Additionally, significant differences regarding the magnetic coupling between the Nia-C state and [4Fe4S] clusters were observed in the reduced form of the MBH. The spectroscopic properties are discussed with regard to the unusual oxygen tolerance of this hydrogenase and in comparison with those of the solubilized, dimeric form of the MBH.
Collapse
Affiliation(s)
- Miguel Saggu
- From the Institut für Chemie, Technische Universität Berlin, PC14, Strasse des 17. Juni 135, D-10623 Berlin
| | - Ingo Zebger
- From the Institut für Chemie, Technische Universität Berlin, PC14, Strasse des 17. Juni 135, D-10623 Berlin.
| | - Marcus Ludwig
- Institute of Biology, Department of Microbiology, Humboldt-Universität zu Berlin, Chausseestrasse 117, D-10115 Berlin, Germany
| | - Oliver Lenz
- Institute of Biology, Department of Microbiology, Humboldt-Universität zu Berlin, Chausseestrasse 117, D-10115 Berlin, Germany
| | - Bärbel Friedrich
- Institute of Biology, Department of Microbiology, Humboldt-Universität zu Berlin, Chausseestrasse 117, D-10115 Berlin, Germany
| | - Peter Hildebrandt
- From the Institut für Chemie, Technische Universität Berlin, PC14, Strasse des 17. Juni 135, D-10623 Berlin
| | - Friedhelm Lendzian
- From the Institut für Chemie, Technische Universität Berlin, PC14, Strasse des 17. Juni 135, D-10623 Berlin.
| |
Collapse
|
19
|
Peters JW. Carbon Monoxide and Cyanide Ligands in the Active Site of [FeFe]-Hydrogenases. METAL-CARBON BONDS IN ENZYMES AND COFACTORS 2009. [DOI: 10.1039/9781847559333-00179] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The [FeFe]-hydrogenases, although share common features when compared to other metal containing hydrogenases, clearly have independent evolutionary origins. Examples of [FeFe]-hydrogenases have been characterized in detail by biochemical and spectroscopic approaches and the high resolution structures of two examples have been determined. The active site H-cluster is a complex bridged metal assembly in which a [4Fe-4S] cubane is bridged to a 2Fe subcluster with unique non-protein ligands including carbon monoxide, cyanide, and a five carbon dithiolate. Carbon monoxide and cyanide ligands as a component of a native active metal center is a property unique to the metal containing hydrogenases and there has been considerable attention to the characterization of the H-cluster at the level of electronic structure and mechanism as well as to defining the biological means to synthesize such a unique metal cluster. The chapter describes the structural architecture of [FeFe]-hydrogenases and key spectroscopic observations that have afforded the field with a fundamental basis for understanding the relationship between structure and reactivity of the H-cluster. In addition, the results and ideas concerning the topic of H-cluster biosynthesis as an emerging and fascinating area of research, effectively reinforcing the potential linkage between iron-sulfur biochemistry to the role of iron-sulfur minerals in prebiotic chemistry and the origin of life.
Collapse
Affiliation(s)
- John W. Peters
- Montana State University, Department of Chemistry and Biochemistry and the Astrobiology Biogeocatalysis Research Center Bozeman, MT 59717 USA
| |
Collapse
|
20
|
An Autocatalytic Mechanism for NiFe-Hydrogenase: Reduction to Ni(I) Followed by Oxidative Addition. Biochemistry 2009; 48:1056-66. [DOI: 10.1021/bi801218n] [Citation(s) in RCA: 89] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
21
|
Kellers P, Pandelia ME, Currell LJ, Görner H, Lubitz W. FTIR study on the light sensitivity of the [NiFe] hydrogenase from Desulfovibrio vulgaris Miyazaki F: Ni–C to Ni–L photoconversion, kinetics of proton rebinding and H/D isotope effect. Phys Chem Chem Phys 2009; 11:8680-3. [DOI: 10.1039/b913635e] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
22
|
Valdés J, Pedroso I, Quatrini R, Dodson RJ, Tettelin H, Blake R, Eisen JA, Holmes DS. Acidithiobacillus ferrooxidans metabolism: from genome sequence to industrial applications. BMC Genomics 2008; 9:597. [PMID: 19077236 PMCID: PMC2621215 DOI: 10.1186/1471-2164-9-597] [Citation(s) in RCA: 315] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2008] [Accepted: 12/11/2008] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Acidithiobacillus ferrooxidans is a major participant in consortia of microorganisms used for the industrial recovery of copper (bioleaching or biomining). It is a chemolithoautrophic, gamma-proteobacterium using energy from the oxidation of iron- and sulfur-containing minerals for growth. It thrives at extremely low pH (pH 1-2) and fixes both carbon and nitrogen from the atmosphere. It solubilizes copper and other metals from rocks and plays an important role in nutrient and metal biogeochemical cycling in acid environments. The lack of a well-developed system for genetic manipulation has prevented thorough exploration of its physiology. Also, confusion has been caused by prior metabolic models constructed based upon the examination of multiple, and sometimes distantly related, strains of the microorganism. RESULTS The genome of the type strain A. ferrooxidans ATCC 23270 was sequenced and annotated to identify general features and provide a framework for in silico metabolic reconstruction. Earlier models of iron and sulfur oxidation, biofilm formation, quorum sensing, inorganic ion uptake, and amino acid metabolism are confirmed and extended. Initial models are presented for central carbon metabolism, anaerobic metabolism (including sulfur reduction, hydrogen metabolism and nitrogen fixation), stress responses, DNA repair, and metal and toxic compound fluxes. CONCLUSION Bioinformatics analysis provides a valuable platform for gene discovery and functional prediction that helps explain the activity of A. ferrooxidans in industrial bioleaching and its role as a primary producer in acidic environments. An analysis of the genome of the type strain provides a coherent view of its gene content and metabolic potential.
Collapse
Affiliation(s)
- Jorge Valdés
- Center for Bioinformatics and Genome Biology, Fundación Ciencia para la Vida, Facultad de Ciencias de la Salud, Universidad Andres Bello, Santiago, Chile.
| | | | | | | | | | | | | | | |
Collapse
|
23
|
Lubitz W, Reijerse E, van Gastel M. [NiFe] and [FeFe] Hydrogenases Studied by Advanced Magnetic Resonance Techniques. Chem Rev 2007; 107:4331-65. [PMID: 17845059 DOI: 10.1021/cr050186q] [Citation(s) in RCA: 376] [Impact Index Per Article: 22.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Wolfgang Lubitz
- Max-Planck-Institut für Bioanorganische Chemie, Stiftstrasse 34-36, D-45470 Mülheim an der Ruhr, Germany
| | | | | |
Collapse
|