1
|
Gevorgyan H, Baghdasaryan L, Trchounian K. Regulation of metabolism and proton motive force generation during mixed carbon fermentation by an Escherichia coli strain lacking the F OF 1-ATPase. BIOCHIMICA ET BIOPHYSICA ACTA. BIOENERGETICS 2024; 1865:149034. [PMID: 38354879 DOI: 10.1016/j.bbabio.2024.149034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 01/15/2024] [Accepted: 02/09/2024] [Indexed: 02/16/2024]
Abstract
Proton FOF1-ATPase is the key enzyme in E. coli under fermentative conditions. In this study the role of E. coli proton ATPase in the μ and formation of metabolic pathways during the fermentation of mixture of glucose, glycerol and formate using the DK8 (lacking FOF1) mutant strain was investigated. It was shown that the contribution of FOF1-ATPase in the specific growth rate was ∼45 %. Formate was not taken up in the DK8 strain during the initial hours of the growth. The utilization rates of glucose and glycerol were unchanged in DK8, however, the production of succinate, lactate and ethanol was decreased causing a reduction of the redox state up to -450 mV. Moreover, the contribution of FOF1-ATPase in the interplay between H+ and H2 cycles was described depending on the bacterial growth phase and main utilizing substrate. Besides, the H2 production rate in the DK8 strain was decreased by ∼60 % at 20 h and was absent at 72 h. Δp was decreased from -157 ± 4.8 mV to -140 ± 4.2 mV at 20 h and from -195 ± 5.9 mV to -148 ± 4.4 mV at 72 h, compared to WT. Taken together it can be concluded that during fermentation of mixed carbon sources metabolic cross talk between FOF1-ATPase-TrkA-Hyd-Fdh-H is taking place for maintaining the cell energy balance via regulation proton motive force.
Collapse
Affiliation(s)
- Heghine Gevorgyan
- Department of Biochemistry, Microbiology and Biotechnology, Faculty of Biology, Yerevan State University, 0025 Yerevan, Armenia; Scientific-Research Institute of Biology, Faculty of Biology, Yerevan State University, 0025 Yerevan, Armenia; Microbial Biotechnologies and Biofuel Innovation Center, Yerevan State University, 0025 Yerevan, Armenia
| | - Lilit Baghdasaryan
- Department of Biochemistry, Microbiology and Biotechnology, Faculty of Biology, Yerevan State University, 0025 Yerevan, Armenia; Microbial Biotechnologies and Biofuel Innovation Center, Yerevan State University, 0025 Yerevan, Armenia
| | - Karen Trchounian
- Department of Biochemistry, Microbiology and Biotechnology, Faculty of Biology, Yerevan State University, 0025 Yerevan, Armenia; Scientific-Research Institute of Biology, Faculty of Biology, Yerevan State University, 0025 Yerevan, Armenia; Microbial Biotechnologies and Biofuel Innovation Center, Yerevan State University, 0025 Yerevan, Armenia.
| |
Collapse
|
2
|
Stepwise assembly of the active site of [NiFe]-hydrogenase. Nat Chem Biol 2023; 19:498-506. [PMID: 36702959 DOI: 10.1038/s41589-022-01226-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 11/16/2022] [Indexed: 01/27/2023]
Abstract
[NiFe]-hydrogenases are biotechnologically relevant enzymes catalyzing the reversible splitting of H2 into 2e- and 2H+ under ambient conditions. Catalysis takes place at the heterobimetallic NiFe(CN)2(CO) center, whose multistep biosynthesis involves careful handling of two transition metals as well as potentially harmful CO and CN- molecules. Here, we investigated the sequential assembly of the [NiFe] cofactor, previously based on primarily indirect evidence, using four different purified maturation intermediates of the catalytic subunit, HoxG, of the O2-tolerant membrane-bound hydrogenase from Cupriavidus necator. These included the cofactor-free apo-HoxG, a nickel-free version carrying only the Fe(CN)2(CO) fragment, a precursor that contained all cofactor components but remained redox inactive and the fully mature HoxG. Through biochemical analyses combined with comprehensive spectroscopic investigation using infrared, electronic paramagnetic resonance, Mössbauer, X-ray absorption and nuclear resonance vibrational spectroscopies, we obtained detailed insight into the sophisticated maturation process of [NiFe]-hydrogenase.
Collapse
|
3
|
Soboh B, Adrian L, Stripp ST. An in vitro reconstitution system to monitor iron transfer to the active site during the maturation of [NiFe]-hydrogenase. J Biol Chem 2022; 298:102291. [PMID: 35868564 PMCID: PMC9418501 DOI: 10.1016/j.jbc.2022.102291] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 07/13/2022] [Accepted: 07/16/2022] [Indexed: 11/29/2022] Open
Abstract
[NiFe]-hydrogenases comprise a small and a large subunit. The latter harbors the biologically unique [NiFe](CN)2CO active site cofactor. The maturation process includes the assembly of the [Fe](CN)2CO cofactor precursor, nickel binding, endoproteolytic cleavage of the large subunit, and dimerization with the small subunit to yield active enzyme. The biosynthesis of the [Fe](CN)2CO moiety of [NiFe]-Hydrogenase 1 (Hyd-1) and Hyd-2 occurs on the scaffold complex HybG-HypD (GD), whereas the HypC-HypD complex (CD) is specific for the assembly of Hyd-3. The metabolic source and the route for delivering iron to the active site remain unclear. To investigate the maturation process of O2-tolerant Hyd-1 from Escherichia coli, we developed an enzymatic in vitro reconstitution system that allows for the synthesis of Hyd-1 using only purified components. Together with this in vitro reconstitution system, we employed biochemical analyses, infrared spectroscopy (ATR FTIR), mass spectrometry, and microscale thermophoresis (MST) to monitor the iron transfer during the maturation process and to understand how the [Fe](CN)2CO cofactor precursor is ultimately incorporated into the large subunit. We demonstrate the direct transfer of iron from 57Fe-labeled GD complex to the large subunit of Hyd-1. Our data reveal that the GD complex exclusively interacts with the large subunit of Hyd-1 and Hyd-2 but not with the large subunit of Hyd-3. Furthermore, we show that the presence of iron in the active site is a prerequisite for nickel insertion. Taken together, these findings reveal how the [Fe](CN)2CO cofactor precursor is transferred and incorporated into the active site of [NiFe]-hydrogenase.
Collapse
Affiliation(s)
- Basem Soboh
- Genetic Biophysics, Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195, Berlin, Germany.
| | - Lorenz Adrian
- Department of Environmental Biotechnology, Helmholtz Centre for Environmental Research - UFZ, Permoserstraße 15, 04318 Leipzig, Germany; Chair of Geobiotechnology, Technische Universität Berlin, Ackerstraße 76, 13355 Berlin, Germany
| | - Sven T Stripp
- Experimental Molecular Biophysics, Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195, Berlin, Germany
| |
Collapse
|
4
|
Fan Q, Caserta G, Lorent C, Zebger I, Neubauer P, Lenz O, Gimpel M. High-Yield Production of Catalytically Active Regulatory [NiFe]-Hydrogenase From Cupriavidus necator in Escherichia coli. Front Microbiol 2022; 13:894375. [PMID: 35572669 PMCID: PMC9100943 DOI: 10.3389/fmicb.2022.894375] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 04/08/2022] [Indexed: 11/13/2022] Open
Abstract
Hydrogenases are biotechnologically relevant metalloenzymes that catalyze the reversible conversion of molecular hydrogen into protons and electrons. The O2-tolerant [NiFe]-hydrogenases from Cupriavidus necator (formerly Ralstonia eutropha) are of particular interest as they maintain catalysis even in the presence of molecular oxygen. However, to meet the demands of biotechnological applications and scientific research, a heterologous production strategy is required to overcome the low production yields in their native host. We have previously used the regulatory hydrogenase (RH) from C. necator as a model for the development of such a heterologous hydrogenase production process in E. coli. Although high protein yields were obtained, the purified enzyme was inactive due to the lack of the catalytic center, which contains an inorganic nickel-iron cofactor. In the present study, we significantly improved the production process to obtain catalytically active RH. We optimized important factors such as O2 content, metal availability, production temperature and time as well as the co-expression of RH-specific maturase genes. The RH was successfully matured during aerobic cultivation of E. coli by co-production of seven hydrogenase-specific maturases and a nickel permease, which was confirmed by activity measurements and spectroscopic investigations of the purified enzyme. The improved production conditions resulted in a high yield of about 80 mg L–1 of catalytically active RH and an up to 160-fold space-time yield in E. coli compared to that in the native host C. necator [<0.1 U (L d) –1]. Our strategy has important implications for the use of E. coli K-12 and B strains in the recombinant production of complex metalloenzymes, and provides a blueprint for the production of catalytically active [NiFe]-hydrogenases in biotechnologically relevant quantities.
Collapse
Affiliation(s)
- Qin Fan
- Chair of Bioprocess Engineering, Department of Biotechnology, Technische Universität Berlin, Berlin, Germany
| | - Giorgio Caserta
- Department of Chemistry, Technische Universität Berlin, Berlin, Germany
| | - Christian Lorent
- Department of Chemistry, Technische Universität Berlin, Berlin, Germany
| | - Ingo Zebger
- Department of Chemistry, Technische Universität Berlin, Berlin, Germany
| | - Peter Neubauer
- Chair of Bioprocess Engineering, Department of Biotechnology, Technische Universität Berlin, Berlin, Germany
| | - Oliver Lenz
- Department of Chemistry, Technische Universität Berlin, Berlin, Germany
| | - Matthias Gimpel
- Chair of Bioprocess Engineering, Department of Biotechnology, Technische Universität Berlin, Berlin, Germany
- *Correspondence: Matthias Gimpel,
| |
Collapse
|
5
|
Finney AJ, Buchanan G, Palmer T, Coulthurst SJ, Sargent F. Activation of a [NiFe]-hydrogenase-4 isoenzyme by maturation proteases. MICROBIOLOGY (READING, ENGLAND) 2020; 166:854-860. [PMID: 32731905 PMCID: PMC7654741 DOI: 10.1099/mic.0.000963] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 07/22/2020] [Indexed: 12/23/2022]
Abstract
Maturation of [NiFe]-hydrogenases often involves specific proteases responsible for cleavage of the catalytic subunits. Escherichia coli HycI is the protease dedicated to maturation of the Hydrogenase-3 isoenzyme, a component of formate hydrogenlyase-1. In this work, it is demonstrated that a Pectobacterium atrosepticum HycI homologue, HyfK, is required for hydrogenase-4 activity, a component of formate hydrogenlyase-2, in that bacterium. The P. atrosepticum ΔhyfK mutant phenotype could be rescued by either P. atrosepticum hyfK or E. coli hycI on a plasmid. Conversely, an E. coli ΔhycI mutant was complemented by either E. coli hycI or P. atrosepticum hyfK in trans. E. coli is a rare example of a bacterium containing both hydrogenase-3 and hydrogenase-4, however the operon encoding hydrogenase-4 has no maturation protease gene. This work suggests HycI should be sufficient for maturation of both E. coli formate hydrogenlyases, however no formate hydrogenlyase-2 activity was detected in any E. coli strains tested here.
Collapse
Affiliation(s)
- Alexander J. Finney
- School of Natural & Environmental Sciences, Faculty of Science, Agriculture & Engineering, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
- School of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland
| | - Grant Buchanan
- School of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland
- Institute of Biosciences, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Tracy Palmer
- School of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland
- Institute of Biosciences, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | | | - Frank Sargent
- School of Natural & Environmental Sciences, Faculty of Science, Agriculture & Engineering, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
- School of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland
| |
Collapse
|
6
|
Caserta G, Lorent C, Ciaccafava A, Keck M, Breglia R, Greco C, Limberg C, Hildebrandt P, Cramer SP, Zebger I, Lenz O. The large subunit of the regulatory [NiFe]-hydrogenase from Ralstonia eutropha - a minimal hydrogenase? Chem Sci 2020; 11:5453-5465. [PMID: 34094072 PMCID: PMC8159394 DOI: 10.1039/d0sc01369b] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
Abstract
Chemically synthesized compounds that are capable of facilitating the reversible splitting of dihydrogen into protons and electrons are rare in chemists' portfolio. The corresponding biocatalysts – hydrogenases – are, however, abundant in the microbial world. [NiFe]-hydrogenases represent a major subclass and display a bipartite architecture, composed of a large subunit, hosting the catalytic NiFe(CO)(CN)2 cofactor, and a small subunit whose iron–sulfur clusters are responsible for electron transfer. To analyze in detail the catalytic competence of the large subunit without its smaller counterpart, we purified the large subunit HoxC of the regulatory [NiFe]-hydrogenase of the model H2 oxidizer Ralstonia eutropha to homogeneity. Metal determination and infrared spectroscopy revealed a stoichiometric loading of the metal cofactor. This enabled for the first time the determination of the UV-visible extinction coefficient of the NiFe(CO)(CN)2 cofactor. Moreover, the absence of disturbing iron–sulfur clusters allowed an unbiased look into the low-spin Fe2+ of the active site by Mössbauer spectroscopy. Isolated HoxC was active in catalytic hydrogen–deuterium exchange, demonstrating its capacity to activate H2. Its catalytic activity was drastically lower than that of the bipartite holoenzyme. This was consistent with infrared and electron paramagnetic resonance spectroscopic observations, suggesting that the bridging position between the active site nickel and iron ions is predominantly occupied by water-derived ligands, even under reducing conditions. In fact, the presence of water-derived ligands bound to low-spin Ni2+ was reflected by the absorption bands occurring in the corresponding UV-vis spectra, as revealed by time-dependent density functional theory calculations conducted on appropriate in silico models. Thus, the isolated large subunits indeed represent simple [NiFe]-hydrogenase models, which could serve as blueprints for chemically synthesized mimics. Furthermore, our data point to a fundamental role of the small subunit in preventing water access to the catalytic center, which significantly increases the H2 splitting capacity of the enzyme. Spectroscopic investigation of an isolated [NiFe]-hydrogenase large subunit enables a unique view of the NiFe(CO)(CN)2 cofactor.![]()
Collapse
Affiliation(s)
- Giorgio Caserta
- Institut für Chemie, Technische Universität Berlin Straße des 17. Juni 135 10623 Berlin Germany
| | - Christian Lorent
- Institut für Chemie, Technische Universität Berlin Straße des 17. Juni 135 10623 Berlin Germany
| | - Alexandre Ciaccafava
- Institut für Chemie, Technische Universität Berlin Straße des 17. Juni 135 10623 Berlin Germany
| | - Matthias Keck
- Department of Chemistry, Humboldt-Universität zu Berlin Brook-Taylor-Straße 2 12489 Berlin Germany
| | - Raffaella Breglia
- Department of Earth and Environmental Sciences, Milano-Bicocca University Piazza della Scienza 1 20126 Milan Italy
| | - Claudio Greco
- Department of Earth and Environmental Sciences, Milano-Bicocca University Piazza della Scienza 1 20126 Milan Italy
| | - Christian Limberg
- Department of Chemistry, Humboldt-Universität zu Berlin Brook-Taylor-Straße 2 12489 Berlin Germany
| | - Peter Hildebrandt
- Institut für Chemie, Technische Universität Berlin Straße des 17. Juni 135 10623 Berlin Germany
| | | | - Ingo Zebger
- Institut für Chemie, Technische Universität Berlin Straße des 17. Juni 135 10623 Berlin Germany
| | - Oliver Lenz
- Institut für Chemie, Technische Universität Berlin Straße des 17. Juni 135 10623 Berlin Germany
| |
Collapse
|
7
|
Hartmann S, Frielingsdorf S, Caserta G, Lenz O. A membrane-bound [NiFe]-hydrogenase large subunit precursor whose C-terminal extension is not essential for cofactor incorporation but guarantees optimal maturation. Microbiologyopen 2020; 9:1197-1206. [PMID: 32180370 PMCID: PMC7294309 DOI: 10.1002/mbo3.1029] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 02/29/2020] [Accepted: 03/02/2020] [Indexed: 01/20/2023] Open
Abstract
[NiFe]‐hydrogenases catalyze the reversible conversion of molecular hydrogen into protons end electrons. This reaction takes place at a NiFe(CN)2(CO) cofactor located in the large subunit of the bipartite hydrogenase module. The corresponding apo‐protein carries usually a C‐terminal extension that is cleaved off by a specific endopeptidase as soon as the cofactor insertion has been accomplished by the maturation machinery. This process triggers complex formation with the small, electron‐transferring subunit of the hydrogenase module, revealing catalytically active enzyme. The role of the C‐terminal extension in cofactor insertion, however, remains elusive. We have addressed this problem by using genetic engineering to remove the entire C‐terminal extension from the apo‐form of the large subunit of the membrane‐bound [NiFe]‐hydrogenase (MBH) from Ralstonia eutropha. Unexpectedly, the MBH holoenzyme derived from this precleaved large subunit was targeted to the cytoplasmic membrane, conferred H2‐dependent growth of the host strain, and the purified protein showed exactly the same catalytic activity as native MBH. The only difference was a reduced hydrogenase content in the cytoplasmic membrane. These results suggest that in the case of the R. eutropha MBH, the C‐terminal extension is dispensable for cofactor insertion and seems to function only as a maturation facilitator.
Collapse
Affiliation(s)
- Sven Hartmann
- Institut für Chemie, Physikalische Chemie, Technische Universität Berlin, Berlin, Germany
| | - Stefan Frielingsdorf
- Institut für Chemie, Physikalische Chemie, Technische Universität Berlin, Berlin, Germany
| | - Giorgio Caserta
- Institut für Chemie, Physikalische Chemie, Technische Universität Berlin, Berlin, Germany
| | - Oliver Lenz
- Institut für Chemie, Physikalische Chemie, Technische Universität Berlin, Berlin, Germany
| |
Collapse
|