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Jiang W, Cai Y, Sun S, Wang W, Tišma M, Baganz F, Hao J. Inactivation of hydrogenase-3 leads to enhancement of 1,3-propanediol and 2,3-butanediol production by Klebsiella pneumoniae. Enzyme Microb Technol 2024; 177:110438. [PMID: 38518554 DOI: 10.1016/j.enzmictec.2024.110438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Revised: 03/16/2024] [Accepted: 03/17/2024] [Indexed: 03/24/2024]
Abstract
Klebsiella pneumoniae can use glucose or glycerol as carbon sources to produce 1,3-propanediol or 2,3-butanediol, respectively. In the metabolism of Klebsiella pneumoniae, hydrogenase-3 is responsible for H2 production from formic acid, but it is not directly related to the synthesis pathways for 1,3-propanediol and 2,3-butanediol. In the first part of this research, hycEFG, which encodes subunits of the enzyme hydrogenase-3, was knocked out, so K. pneumoniae ΔhycEFG lost the ability to produce H2 during cultivation using glycerol as a carbon source. As a consequence, the concentration of 1,3-propanediol increased and the substrate (glycerol) conversion ratio reached 0.587 mol/mol. Then, K. pneumoniae ΔldhAΔhycEFG was constructed to erase lactic acid synthesis which led to the further increase of 1,3-propanediol concentration. A substrate (glycerol) conversion ratio of 0.628 mol/mol in batch conditions was achieved, which was higher compared to the wild type strain (0.545 mol/mol). Furthermore, since adhE encodes an alcohol dehydrogenase that catalyzes ethanol production from acetaldehyde, K. pneumoniae ΔldhAΔadhEΔhycEFG was constructed to prevent ethanol production. Contrary to expectations, this did not lead to a further increase, but to a decrease in 1,3-propanediol production. In the second part of this research, glucose was used as the carbon source to produce 2,3-butanediol. Knocking out hycEFG had distinct positive effect on 2,3-butanediol production. Especially in K. pneumoniae ΔldhAΔadhEΔhycEFG, a substrate (glucose) conversion ratio of 0.730 mol/mol was reached, which is higher compared to wild type strain (0.504 mol/mol). This work suggests that the inactivation of hydrogenase-3 may have a global effect on the metabolic regulation of K. pneumoniae, leading to the improvement of the production of two industrially important bulk chemicals, 1,3-propanediol and 2,3-butanediol.
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Affiliation(s)
- Weiyan Jiang
- Lab of Biorefinery, Shanghai Advanced Research Institute, Chinese Academy of Sciences, No. 99 Haike Road, Pudong, Shanghai 201210, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Yaoyu Cai
- Lab of Biorefinery, Shanghai Advanced Research Institute, Chinese Academy of Sciences, No. 99 Haike Road, Pudong, Shanghai 201210, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Shaoqi Sun
- Lab of Biorefinery, Shanghai Advanced Research Institute, Chinese Academy of Sciences, No. 99 Haike Road, Pudong, Shanghai 201210, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Wenqi Wang
- Lab of Biorefinery, Shanghai Advanced Research Institute, Chinese Academy of Sciences, No. 99 Haike Road, Pudong, Shanghai 201210, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Marina Tišma
- Josip Juraj Strossmayer University of Osijek, Faculty of Food Technology Osijek, Franje Kuhača 18, Osijek HR-31000, Croatia
| | - Frank Baganz
- Department of Biochemical Engineering, University College London, Gordon Street, London WC1H 0AH, UK
| | - Jian Hao
- Lab of Biorefinery, Shanghai Advanced Research Institute, Chinese Academy of Sciences, No. 99 Haike Road, Pudong, Shanghai 201210, PR China; Department of Biochemical Engineering, University College London, Gordon Street, London WC1H 0AH, UK; University of Chinese Academy of Sciences, Beijing 100049, PR China.
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Yang JI, Jung HC, Oh HM, Choi BG, Lee HS, Kang SG. NADP + or CO 2 reduction by frhAGB-encoded hydrogenase through interaction with formate dehydrogenase 3 in the hyperthermophilic archaeon Thermococcus onnurineus NA1. Appl Environ Microbiol 2023; 89:e0147423. [PMID: 37966269 PMCID: PMC10734459 DOI: 10.1128/aem.01474-23] [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: 09/04/2023] [Accepted: 09/23/2023] [Indexed: 11/16/2023] Open
Abstract
IMPORTANCE The strategy using structural homology with the help of structure prediction by AlphaFold was very successful in finding potential targets for the frhAGB-encoded hydrogenase of Thermococcus onnurineus NA1. The finding that the hydrogenase can interact with FdhB to reduce the cofactor NAD(P)+ is significant in that the enzyme can function to supply reducing equivalents, just as F420-reducing hydrogenases in methanogens use coenzyme F420 as an electron carrier. Additionally, it was identified that T. onnurineus NA1 could produce formate from H2 and CO2 by the concerted action of frhAGB-encoded hydrogenase and formate dehydrogenase Fdh3.
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Affiliation(s)
- Ji-in Yang
- Marine Biotechnology Research Center, Korea Institute of Ocean Science & Technology, Busan, South Korea
- Department of Applied Ocean Science, University of Science and Technology, Daejeon, South Korea
| | - Hae-Chang Jung
- Marine Biotechnology Research Center, Korea Institute of Ocean Science & Technology, Busan, South Korea
| | | | - Bo Gyoung Choi
- Marine Biotechnology Research Center, Korea Institute of Ocean Science & Technology, Busan, South Korea
| | - Hyun Sook Lee
- Marine Biotechnology Research Center, Korea Institute of Ocean Science & Technology, Busan, South Korea
- Department of Applied Ocean Science, University of Science and Technology, Daejeon, South Korea
| | - Sung Gyun Kang
- Marine Biotechnology Research Center, Korea Institute of Ocean Science & Technology, Busan, South Korea
- Department of Applied Ocean Science, University of Science and Technology, Daejeon, South Korea
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Nguyen HK, Minato T, Moniruzzaman M, Kiyasu Y, Ogo S, Yoon KS. Selective formate production from H 2 and CO 2 using encapsulated whole-cells under mild reaction conditions. J Biosci Bioeng 2023; 136:182-189. [PMID: 37400329 DOI: 10.1016/j.jbiosc.2023.06.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 06/05/2023] [Accepted: 06/06/2023] [Indexed: 07/05/2023]
Abstract
Biocatalytic CO2 reduction into formate is a crucial strategy for developing clean energy because formate is considered as one of the promising hydrogen storage materials for achieving net-zero carbon emissions. Here, we developed an efficient biocatalytic system to produce formate selectively by coupling two enzymatic activities of H2 oxidation and CO2 reduction using encapsulated bacterial cells of Citrobacter sp. S-77. The encapsulated whole-cell catalyst was made by living cells depositing into polyvinyl alcohol and gellan gum cross-linked by calcium ions to form hydrogel beads. Formate production using encapsulated cells was carried out under the resting state conditions in the gas mixture of H2/CO2 (70:30, v/v%). The whole-cell biocatalyst showed highly efficient and selective catalytic production of formate, reaching the specific rate of formate production of 110 mmol L-1· gprotein-1·h-1 at 30 °C, pH 7.0, and 0.1 MPa. The encapsulated cells can be reused at least 8 times while keeping their high catalytic activities for formate production under mild reaction conditions.
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Affiliation(s)
- Hung Khac Nguyen
- Department of Chemistry and Biochemistry, Graduate School of Engineering, Kyushu University, Japan
| | - Takuo Minato
- Department of Chemistry and Biochemistry, Graduate School of Engineering, Kyushu University, Japan; International Institute for Carbon-Neutral Energy Research (WPI-I(2)CNER), Kyushu University, Japan; Department of Applied Chemistry, Graduate School of Advanced Science and Engineering, Hiroshima University, 1-4-1 Kagamiyama, Higashi-Hiroshima, Hiroshima, 739-8527, Japan
| | - Mohammad Moniruzzaman
- International Institute for Carbon-Neutral Energy Research (WPI-I(2)CNER), Kyushu University, Japan; Mitsui Chemicals, Inc.- Carbon Neutral Research Center (MCI-CNRC), Kyushu University, Japan
| | - Yu Kiyasu
- Department of Chemistry and Biochemistry, Graduate School of Engineering, Kyushu University, Japan
| | - Seiji Ogo
- Department of Chemistry and Biochemistry, Graduate School of Engineering, Kyushu University, Japan; International Institute for Carbon-Neutral Energy Research (WPI-I(2)CNER), Kyushu University, Japan; Center for Small Molecule Energy, Kyushu University, 744 Moto-oka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Ki-Seok Yoon
- Department of Chemistry and Biochemistry, Graduate School of Engineering, Kyushu University, Japan; International Institute for Carbon-Neutral Energy Research (WPI-I(2)CNER), Kyushu University, Japan; Mitsui Chemicals, Inc.- Carbon Neutral Research Center (MCI-CNRC), Kyushu University, Japan.
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Ting WW, Yu JY, Lin YC, Ng IS. Enhanced recombinant carbonic anhydrase in T7RNAP-equipped Escherichia coli W3110 for carbon capture storage and utilization (CCSU). BIORESOURCE TECHNOLOGY 2022; 363:128010. [PMID: 36167176 DOI: 10.1016/j.biortech.2022.128010] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Revised: 09/16/2022] [Accepted: 09/17/2022] [Indexed: 06/16/2023]
Abstract
Sulfurihydrogenibium yellowstonense carbonic anhydrase (SyCA) is a well-known thermophilic CA for carbon mineralization. To broaden the applications of SyCA, the activity of SyCA was improved through stepwise engineering and in different cultural conditions, as well as extended to co-expression with other enzymes. The engineered W3110 strains with 4 different T7 RNA polymerase levels were employed for SyCA production. As a result, the best strain WT7L cultured in modified M9 medium with temperature shifted from 37 to 30 °C after induction increased SyCA activity to 9122 U/mL. The SyCA whole-cell biocatalyst was successfully applied for carbon capture and storage (CCS) of CaCO3. Furthermore, SyCA was applied for low-carbon footprint synthesis of 5-aminolevulinic acid (5-ALA) and cadaverine (DAP) by coupling with ALA synthetase (ALAS) and lysine decarboxylase (CadA), suppressing CO2 release to -6.1 g-CO2/g-ALA and -2.53 g-CO2/g-DAP, respectively. Harnessing a highly active SyCA offers a complete strategy for CCSU in a green process.
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Affiliation(s)
- Wan-Wen Ting
- Department of Chemical Engineering, National Cheng Kung University, Tainan 70101, Taiwan
| | - Jie-Yao Yu
- Department of Chemical Engineering, National Cheng Kung University, Tainan 70101, Taiwan
| | - Yu-Chieh Lin
- Department of Chemical Engineering, National Cheng Kung University, Tainan 70101, Taiwan
| | - I-Son Ng
- Department of Chemical Engineering, National Cheng Kung University, Tainan 70101, Taiwan.
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Steinhilper R, Höff G, Heider J, Murphy BJ. Structure of the membrane-bound formate hydrogenlyase complex from Escherichia coli. Nat Commun 2022; 13:5395. [PMID: 36104349 PMCID: PMC9474812 DOI: 10.1038/s41467-022-32831-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 08/08/2022] [Indexed: 01/30/2023] Open
Abstract
The prototypical hydrogen-producing enzyme, the membrane-bound formate hydrogenlyase (FHL) complex from Escherichia coli, links formate oxidation at a molybdopterin-containing formate dehydrogenase to proton reduction at a [NiFe] hydrogenase. It is of intense interest due to its ability to efficiently produce H2 during fermentation, its reversibility, allowing H2-dependent CO2 reduction, and its evolutionary link to respiratory complex I. FHL has been studied for over a century, but its atomic structure remains unknown. Here we report cryo-EM structures of FHL in its aerobically and anaerobically isolated forms at resolutions reaching 2.6 Å. This includes well-resolved density for conserved loops linking the soluble and membrane arms believed to be essential in coupling enzymatic turnover to ion translocation across the membrane in the complex I superfamily. We evaluate possible structural determinants of the bias toward hydrogen production over its oxidation and describe an unpredicted metal-binding site near the interface of FdhF and HycF subunits that may play a role in redox-dependent regulation of FdhF interaction with the complex. New cryo-EM structures of the formate hydrogenlyase complex from the model bacterium E. coli clarify how electrons and protons move through the complex and are combined to make H2 gas. The complex shows important similarities and differences to related bioenergetic complexes across the tree of life.
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Membrane-anchored HDCR nanowires drive hydrogen-powered CO 2 fixation. Nature 2022; 607:823-830. [PMID: 35859174 DOI: 10.1038/s41586-022-04971-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 06/13/2022] [Indexed: 01/11/2023]
Abstract
Filamentous enzymes have been found in all domains of life, but the advantage of filamentation is often elusive1. Some anaerobic, autotrophic bacteria have an unusual filamentous enzyme for CO2 fixation-hydrogen-dependent CO2 reductase (HDCR)2,3-which directly converts H2 and CO2 into formic acid. HDCR reduces CO2 with a higher activity than any other known biological or chemical catalyst4,5, and it has therefore gained considerable interest in two areas of global relevance: hydrogen storage and combating climate change by capturing atmospheric CO2. However, the mechanistic basis of the high catalytic turnover rate of HDCR has remained unknown. Here we use cryo-electron microscopy to reveal the structure of a short HDCR filament from the acetogenic bacterium Thermoanaerobacter kivui. The minimum repeating unit is a hexamer that consists of a formate dehydrogenase (FdhF) and two hydrogenases (HydA2) bound around a central core of hydrogenase Fe-S subunits, one HycB3 and two HycB4. These small bacterial polyferredoxin-like proteins oligomerize through their C-terminal helices to form the backbone of the filament. By combining structure-directed mutagenesis with enzymatic analysis, we show that filamentation and rapid electron transfer through the filament enhance the activity of HDCR. To investigate the structure of HDCR in situ, we imaged T. kivui cells with cryo-electron tomography and found that HDCR filaments bundle into large ring-shaped superstructures attached to the plasma membrane. This supramolecular organization may further enhance the stability and connectivity of HDCR to form a specialized metabolic subcompartment within the cell.
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Arthur R, Antonczyk S, Off S, Scherer PA. Mesophilic and Thermophilic Anaerobic Digestion of Wheat Straw in a CSTR System with 'Synthetic Manure': Impact of Nickel and Tungsten on Methane Yields, Cell Count, and Microbiome. Bioengineering (Basel) 2022; 9:bioengineering9010013. [PMID: 35049722 PMCID: PMC8772805 DOI: 10.3390/bioengineering9010013] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 12/23/2021] [Accepted: 12/28/2021] [Indexed: 11/16/2022] Open
Abstract
Lignocellulosic residues, such as straw, are currently considered as candidates for biogas production. Therefore, straw fermentations were performed to quantitatively estimate methane yields and cell counts, as well as to qualitatively determine the microbiome. Six fully automated, continuously stirred biogas reactors were used: three mesophilic (41 °C) and three thermophilic (58 °C). They were fed every 8 h with milled wheat straw suspension in a defined, buffered salt solution, called 'synthetic manure'. Total reflection X-ray fluorescence spectrometry analyses showed nickel and tungsten deficiency in the straw suspension. Supplementation of nickel and subsequently tungsten, or with an increasing combined dosage of both elements, resulted in a final concentration of approximately 0.1 mg/L active, dissolved tungsten ions, which caused an increase of the specific methane production, up to 63% under mesophilic and 31% under thermophilic conditions. That is the same optimal range for pure cultures of methanogens or bacteria found in literature. A simultaneous decrease of volatile fatty acids occurred. The Ni/W effect occurred with all three organic loading rates, being 4.5, 7.5, and 9.0 g volatile solids per litre and day, with a concomitant hydraulic retention time of 18, 10, or 8 days, respectively. A maximum specific methane production of 0.254 m3 CH4, under standard temperature and pressure per kg volatile solids (almost 90% degradation), was obtained. After the final supplementation of tungsten, the cell counts of methanogens increased by 300%, while the total microbial cell counts increased by only 3-62%. The mesophilic methanogenic microflora was shifted from the acetotrophic Methanosaeta to the hydrogenotrophic Methanoculleus (85%) by tungsten, whereas the H2-CO2-converter, Methanothermobacter, always dominated in the thermophilic fermenters.
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Affiliation(s)
- Richard Arthur
- Energy Systems Engineering Department, Koforidua Technical University, Koforidua P.O. Box KF 981, Ghana;
| | - Sebastian Antonczyk
- Research Center for Biomass Utilization, Faculty Life Sciences, Hamburg University of Applied Sciences (HAW), 20099 Hamburg, Germany; (S.A.); (S.O.)
| | - Sandra Off
- Research Center for Biomass Utilization, Faculty Life Sciences, Hamburg University of Applied Sciences (HAW), 20099 Hamburg, Germany; (S.A.); (S.O.)
| | - Paul A. Scherer
- Research Center for Biomass Utilization, Faculty Life Sciences, Hamburg University of Applied Sciences (HAW), 20099 Hamburg, Germany; (S.A.); (S.O.)
- Correspondence:
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