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Zhai Y, Tong S, Chen L, Zhang Y, Amin FR, Khalid H, Liu F, Duan Y, Chen W, Chen G, Li D. The enhancement of energy supply in syngas-fermenting microorganisms. ENVIRONMENTAL RESEARCH 2024; 252:118813. [PMID: 38574985 DOI: 10.1016/j.envres.2024.118813] [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: 11/29/2023] [Revised: 03/25/2024] [Accepted: 03/26/2024] [Indexed: 04/06/2024]
Abstract
After the second industrial revolution, social productivity developed rapidly, and the use of fossil fuels such as coal, oil, and natural gas increased greatly in industrial production. The burning of these fossil fuels releases large amounts of greenhouse gases such as CO2, which has caused greenhouse effects and global warming. This has endangered the planet's ecological balance and brought many species, including animals and plants, to the brink of extinction. Thus, it is crucial to address this problem urgently. One potential solution is the use of syngas fermentation with microbial cell factories. This process can produce chemicals beneficial to humans, such as ethanol as a fuel while consuming large quantities of harmful gases, CO and CO2. However, syngas-fermenting microorganisms often face a metabolic energy deficit, resulting in slow cell growth, metabolic disorders, and low product yields. This problem limits the large-scale industrial application of engineered microorganisms. Therefore, it is imperative to address the energy barriers of these microorganisms. This paper provides an overview of the current research progress in addressing energy barriers in bacteria, including the efficient capture of external energy and the regulation of internal energy metabolic flow. Capturing external energy involves summarizing studies on overexpressing natural photosystems and constructing semiartificial photosynthesis systems using photocatalysts. The regulation of internal energy metabolic flows involves two parts: regulating enzymes and metabolic pathways. Finally, the article discusses current challenges and future perspectives, with a focus on achieving both sustainability and profitability in an economical and energy-efficient manner. These advancements can provide a necessary force for the large-scale industrial application of syngas fermentation microbial cell factories.
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Affiliation(s)
- Yida Zhai
- School of Marine Science and Technology, Harbin Institute of Technology (Weihai), Weihai, 264209, PR China; School of Environment, Harbin Institute of Technology, Harbin, 150090, PR China; Tianjin Key Laboratory for Industrial Biological System and Bioprocessing Engineering, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, PR China
| | - Sheng Tong
- Tianjin Key Laboratory for Industrial Biological System and Bioprocessing Engineering, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, PR China
| | - Limei Chen
- Tianjin Key Laboratory for Industrial Biological System and Bioprocessing Engineering, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, PR China
| | - Yuan Zhang
- Tianjin Key Laboratory for Industrial Biological System and Bioprocessing Engineering, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, PR China
| | - Farrukh Raza Amin
- Tianjin Key Laboratory for Industrial Biological System and Bioprocessing Engineering, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, PR China
| | - Habiba Khalid
- Tianjin Key Laboratory for Industrial Biological System and Bioprocessing Engineering, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, PR China
| | - Fuguo Liu
- School of Marine Science and Technology, Harbin Institute of Technology (Weihai), Weihai, 264209, PR China; School of Environment, Harbin Institute of Technology, Harbin, 150090, PR China
| | - Yu Duan
- School of Marine Science and Technology, Harbin Institute of Technology (Weihai), Weihai, 264209, PR China; School of Environment, Harbin Institute of Technology, Harbin, 150090, PR China; Tianjin Key Laboratory for Industrial Biological System and Bioprocessing Engineering, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, PR China
| | - Wuxi Chen
- Tianjin Key Laboratory for Industrial Biological System and Bioprocessing Engineering, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, PR China
| | - Guofu Chen
- School of Marine Science and Technology, Harbin Institute of Technology (Weihai), Weihai, 264209, PR China.
| | - Demao Li
- Tianjin Key Laboratory for Industrial Biological System and Bioprocessing Engineering, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, PR China.
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Biological Hydrogen Production by Dark Fermentation in a Stirred Tank Reactor and Its Correlation with the pH Time Evolution. Catalysts 2022. [DOI: 10.3390/catal12111366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Dark fermentation is a hydrogen generating process carried out by anaerobic spore-forming bacteria that metabolize carbon sources producing gas and short-chain acids. The process can be controlled, and the hydrogen harvested if bacteria are grown in a reactor with favorable conditions. In this work, bacteria selected from natural sources were grown with a defined culture media, while pH was monitored, with the aim of relating the amount of generated hydrogen to the increase in hydron ion concentration. Therefore, a model based on the acid-base species mass balance is proposed and solved to estimate the lag phase time and measure the hydrogen production efficiency and kinetics. Hydrogen production in a stirred batch reactor was performed for 150–200 h, at given operating conditions using a previously defined growth media, to validate the model. Using the proposed model, the cumulated moles of produced hydrogen correlate well with those predicted from the pH curve. Hence, the modified Gompertz model parameters, largely used for describing the hydrogen generation kinetics by dark fermentation, were estimated from the pH curve and from the experimentally measured generated hydrogen. Satisfactory agreement was found, thus, validating the method.
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Lee H, Bae J, Jin S, Kang S, Cho BK. Engineering Acetogenic Bacteria for Efficient One-Carbon Utilization. Front Microbiol 2022; 13:865168. [PMID: 35615514 PMCID: PMC9124964 DOI: 10.3389/fmicb.2022.865168] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 04/19/2022] [Indexed: 12/03/2022] Open
Abstract
C1 gases, including carbon dioxide (CO2) and carbon monoxide (CO), are major contributors to climate crisis. Numerous studies have been conducted to fix and recycle C1 gases in order to solve this problem. Among them, the use of microorganisms as biocatalysts to convert C1 gases to value-added chemicals is a promising solution. Acetogenic bacteria (acetogens) have received attention as high-potential biocatalysts owing to their conserved Wood–Ljungdahl (WL) pathway, which fixes not only CO2 but also CO. Although some metabolites have been produced via C1 gas fermentation on an industrial scale, the conversion of C1 gases to produce various biochemicals by engineering acetogens has been limited. The energy limitation of acetogens is one of the challenges to overcome, as their metabolism operates at a thermodynamic limit, and the low solubility of gaseous substrates results in a limited supply of cellular energy. This review provides strategies for developing efficient platform strains for C1 gas conversion, focusing on engineering the WL pathway. Supplying liquid C1 substrates, which can be obtained from CO2, or electricity is introduced as a strategy to overcome the energy limitation. Future prospective approaches on engineering acetogens based on systems and synthetic biology approaches are also discussed.
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Affiliation(s)
- Hyeonsik Lee
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Jiyun Bae
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Sangrak Jin
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Seulgi Kang
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Byung-Kwan Cho
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
- KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
- *Correspondence: Byung-Kwan Cho,
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Yi J, Huang H, Liang J, Wang R, Liu Z, Li F, Wang S. A Heterodimeric Reduced-Ferredoxin-Dependent Methylenetetrahydrofolate Reductase from Syngas-Fermenting Clostridium ljungdahlii. Microbiol Spectr 2021; 9:e0095821. [PMID: 34643446 PMCID: PMC8515935 DOI: 10.1128/spectrum.00958-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Accepted: 08/31/2021] [Indexed: 11/20/2022] Open
Abstract
The strict anaerobe Clostridium ljungdahlii can ferment CO or H2/CO2 via the Wood-Ljungdahl pathway to acetate, ethanol, and 2,3-butanediol. This ability has attracted considerable interest, since it can be used for syngas fermentation to produce biofuels and biochemicals. However, the key enzyme methylenetetrahydrofolate reductase (MTHFR) in the Wood-Ljungdahl pathway of the strain has not been characterized, and its physiological electron donor is unclear. In this study, we purified the enzyme 46-fold with a benzyl viologen reduction activity of 41.2 U/mg from C. ljungdahlii cells grown on CO. It is composed of two subunits, MetF (31.5 kDa) and MetV (23.5 kDa), and has an apparent molecular mass of 62.2 kDa. The brownish yellow protein contains 0.73 flavin mononucleotide (FMN) and 7.4 Fe, in agreement with the prediction that MetF binds one flavin and MetV binds two [4Fe4S] clusters. It cannot use NAD(P)H as its electron donor or catalyze an electron-bifurcating reaction in combination with ferredoxin as an electron acceptor. The reduced recombinant ferredoxin, flavodoxin, and thioredoxin of C. ljungdahlii can serve as electron donors with specific activities of 91.2, 22.1, and 7.4 U/mg, respectively. The apparent Km values for reduced ferredoxin and flavodoxin were around 1.46 μM and 0.73 μM, respectively. Subunit composition and phylogenetic analysis showed that the enzyme from C. ljungdahlii belongs to MetFV-type MTHFR, which is a heterodimer, and uses reduced ferredoxin as its electron donor. Based on these results, we discuss the energy metabolism of C. ljungdahlii when it grows on CO or H2 plus CO2. IMPORTANCE Syngas, a mixture of CO, CO2, and H2, is the main component of steel mill waste gas and also can be generated by the gasification of biomass and urban domestic waste. Its fermentation to biofuels and biocommodities has attracted attention due to the economic and environmental benefits of this process. Clostridium ljungdahlii is one of the superior acetogens used in the technology. However, the biochemical mechanism of its gas fermentation via the Wood-Ljungdahl pathway is not completely clear. In this study, the key enzyme, methylenetetrahydrofolate reductase (MTHFR), was characterized and found to be a non-electron-bifurcating heterodimer with reduced ferredoxin as its electron donor, representing another example of MetFV-type MTHFR. The findings will form the basis for a deeper understanding of the energy metabolism of syngas fermentation by C. ljungdahlii, which is valuable for developing metabolic engineering strains and efficient syngas fermentation technologies.
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Affiliation(s)
- Jihong Yi
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, People’s Republic of China
| | - Haiyan Huang
- School of Basic Medicine, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, People’s Republic of China
| | - Jiyu Liang
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, People’s Republic of China
| | - Rufei Wang
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, People’s Republic of China
| | - Ziyong Liu
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, People’s Republic of China
| | - Fuli Li
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, People’s Republic of China
| | - Shuning Wang
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, People’s Republic of China
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Energy conservation under extreme energy limitation: the role of cytochromes and quinones in acetogenic bacteria. Extremophiles 2021; 25:413-424. [PMID: 34480656 PMCID: PMC8578096 DOI: 10.1007/s00792-021-01241-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 08/26/2021] [Indexed: 11/10/2022]
Abstract
Acetogenic bacteria are a polyphyletic group of organisms that fix carbon dioxide under anaerobic, non-phototrophic conditions by reduction of two mol of CO2 to acetyl-CoA via the Wood–Ljungdahl pathway. This pathway also allows for lithotrophic growth with H2 as electron donor and this pathway is considered to be one of the oldest, if not the oldest metabolic pathway on Earth for CO2 reduction, since it is coupled to the synthesis of ATP. How ATP is synthesized has been an enigma for decades, but in the last decade two ferredoxin-dependent respiratory chains were discovered. Those respiratory chains comprise of a cytochrome-free, ferredoxin-dependent respiratory enzyme complex, which is either the Rnf or Ech complex. However, it was discovered already 50 years ago that some acetogens contain cytochromes and quinones, but their role had only a shadowy existence. Here, we review the literature on the characterization of cytochromes and quinones in acetogens and present a hypothesis that they may function in electron transport chains in addition to Rnf and Ech.
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Öppinger C, Kremp F, Müller V. Is reduced ferredoxin the physiological electron donor for MetVF-type methylenetetrahydrofolate reductases in acetogenesis? A hypothesis. Int Microbiol 2021; 25:75-88. [PMID: 34255221 PMCID: PMC8760232 DOI: 10.1007/s10123-021-00190-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 06/24/2021] [Accepted: 06/25/2021] [Indexed: 01/22/2023]
Abstract
The methylene-tetrahydrofolate reductase (MTHFR) is a key enzyme in acetogenic CO2 fixation. The MetVF-type enzyme has been purified from four different species and the physiological electron donor was hypothesized to be reduced ferredoxin. We have purified the MTHFR from Clostridium ljungdahlii to apparent homogeneity. It is a dimer consisting of two of MetVF heterodimers, has 14.9 ± 0.2 mol iron per mol enzyme, 16.2 ± 1.0 mol acid-labile sulfur per mol enzyme, and contains 1.87 mol FMN per mol dimeric heterodimer. NADH and NADPH were not used as electron donor, but reduced ferredoxin was. Based on the published electron carrier specificities for Clostridium formicoaceticum, Thermoanaerobacter kivui, Eubacterium callanderi, and Clostridium aceticum, we provide evidence using metabolic models that reduced ferredoxin cannot be the physiological electron donor in vivo, since growth by acetogenesis from H2 + CO2 has a negative ATP yield. We discuss the possible basis for the discrepancy between in vitro and in vivo functions and present a model how the MetVF-type MTHFR can be incorporated into the metabolism, leading to a positive ATP yield. This model is also applicable to acetogenesis from other substrates and proves to be feasible also to the Ech-containing acetogen T. kivui as well as to methanol metabolism in E. callanderi.
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Affiliation(s)
- Christian Öppinger
- Department of Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Max-von-Laue Str. 9, 60438, Frankfurt, Germany
| | - Florian Kremp
- Department of Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Max-von-Laue Str. 9, 60438, Frankfurt, Germany
| | - Volker Müller
- Department of Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Max-von-Laue Str. 9, 60438, Frankfurt, Germany.
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Dietrich HM, Kremp F, Öppinger C, Ribaric L, Müller V. Biochemistry of methanol-dependent acetogenesis in Eubacterium callanderi KIST612. Environ Microbiol 2021; 23:4505-4517. [PMID: 34125457 DOI: 10.1111/1462-2920.15643] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 06/13/2021] [Indexed: 11/26/2022]
Abstract
Methanol is the simplest of all alcohols, is universally distributed in anoxic sediments as a result of plant material decomposition and is constantly attracting attention as an interesting substrate for anaerobes like acetogens that can convert bio-renewable methanol into value-added chemicals. A major drawback in the development of environmentally friendly but economically attractive biotechnological processes is the present lack of information on biochemistry and bioenergetics during methanol conversion in these bacteria. The mesophilic acetogen Eubacterium callanderi KIST612 is naturally able to consume methanol and produce acetate as well as butyrate. To grasp the full potential of methanol-based production of chemicals, we analysed the genes and enzymes involved in methanol conversion to acetate and identified the redox carriers involved. We will display a complete model for methanol-derived acetogenesis and butyrogenesis in Eubacterium callanderi KIST612, tracing the electron transfer routes and shed light on the bioenergetics during the process.
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Affiliation(s)
- Helge M Dietrich
- Department of Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Max-von-Laue Str. 9, Frankfurt, D-60438, Germany
| | - Florian Kremp
- Department of Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Max-von-Laue Str. 9, Frankfurt, D-60438, Germany
| | - Christian Öppinger
- Department of Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Max-von-Laue Str. 9, Frankfurt, D-60438, Germany
| | - Luna Ribaric
- Department of Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Max-von-Laue Str. 9, Frankfurt, D-60438, Germany
| | - Volker Müller
- Department of Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Max-von-Laue Str. 9, Frankfurt, D-60438, Germany
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