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Li J, Xiang S, Li Y, Cheng R, Lai Q, Wang L, Li G, Dong C, Shao Z. Arcobacteraceae are ubiquitous mixotrophic bacteria playing important roles in carbon, nitrogen, and sulfur cycling in global oceans. mSystems 2024:e0051324. [PMID: 38904399 DOI: 10.1128/msystems.00513-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Accepted: 05/14/2024] [Indexed: 06/22/2024] Open
Abstract
Mixotrophy is an important trophic strategy for bacterial survival in the ocean. However, the global relevance and identity of the major mixotrophic taxa remain largely elusive. Here, we combined phylogenetic, metagenomic, and metatranscriptomic analyses to characterize ubiquitous Arcobacteraceae based on our deep-sea in situ incubations and the global data. The phylogenomic tree of Arcobacteraceae is divided into three large clades, among which members of clades A and B are almost all from terrestrial environments, while those of clade C are widely distributed in various marine habitats in addition to some terrestrial origins. All clades harbor genes putatively involved in chitin degradation, sulfide oxidation, hydrogen oxidation, thiosulfate oxidation, denitrification, dissimilatory nitrate reduction to ammonium, microaerophilic respiration, and metal (iron/manganese) reduction. Additionally, in clade C, more unique pathways were retrieved, including thiosulfate disproportionation, ethanol fermentation, methane oxidation, fatty acid oxidation, cobalamin synthesis, and dissimilatory reductions of sulfate, perchlorate, and arsenate. Within this clade, two mixotrophic Candidatus genera represented by UBA6211 and CAIJNA01 harbor genes putatively involved in the reverse tricarboxylic acid pathway for carbon fixation. Moreover, the metatranscriptomic data in deep-sea in situ incubations indicated that the latter genus is a mixotroph that conducts carbon fixation by coupling sulfur oxidation and denitrification and metabolizing organic matter. Furthermore, global metatranscriptomic data confirmed the ubiquitous distribution and global relevance of Arcobacteraceae in the expression of those corresponding genes across all oceanic regions and depths. Overall, these results highlight the contribution of previously unrecognized Arcobacteraceae to carbon, nitrogen, and sulfur cycling in global oceans.IMPORTANCEMarine microorganisms exert a profound influence on global carbon cycling and ecological relationships. Mixotrophy, characterized by the simultaneous utilization of both autotrophic and heterotrophic nutrition, has a significant impact on the global carbon cycling. This report characterizes a group of uncultivated bacteria Arcobacteraceae that thrived on the "hot time" of bulky particulate organic matter and exhibited mixotrophic strategy during the in situ organic mineralization. Compared with clades A and B, more unique metabolic pathways were retrieved in clade C, including the reverse tricarboxylic acid pathway for carbon fixation, thiosulfate disproportionation, methane oxidation, and fatty acid oxidation. Global metatranscriptomic data from the Tara Oceans expeditions confirmed the ubiquitous distribution and extensive transcriptional activity of Arcobacteraceae with the expression of genes putatively involved in carbon fixation, methane oxidation, multiple sulfur compound oxidation, and denitrification across all oceanic regions and depths.
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Affiliation(s)
- Jianyang Li
- Key Laboratory of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources of Fujian Province, Third Institute of Oceanography, Ministry of Natural Resources of PR China, Xiamen, China
| | - Shizheng Xiang
- Key Laboratory of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources of Fujian Province, Third Institute of Oceanography, Ministry of Natural Resources of PR China, Xiamen, China
| | - Yufei Li
- Key Laboratory of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources of Fujian Province, Third Institute of Oceanography, Ministry of Natural Resources of PR China, Xiamen, China
| | - Ruolin Cheng
- Key Laboratory of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources of Fujian Province, Third Institute of Oceanography, Ministry of Natural Resources of PR China, Xiamen, China
| | - Qiliang Lai
- Key Laboratory of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources of Fujian Province, Third Institute of Oceanography, Ministry of Natural Resources of PR China, Xiamen, China
| | - Liping Wang
- Key Laboratory of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources of Fujian Province, Third Institute of Oceanography, Ministry of Natural Resources of PR China, Xiamen, China
| | - Guizhen Li
- Key Laboratory of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources of Fujian Province, Third Institute of Oceanography, Ministry of Natural Resources of PR China, Xiamen, China
| | - Chunming Dong
- Key Laboratory of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources of Fujian Province, Third Institute of Oceanography, Ministry of Natural Resources of PR China, Xiamen, China
| | - Zongze Shao
- Key Laboratory of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources of Fujian Province, Third Institute of Oceanography, Ministry of Natural Resources of PR China, Xiamen, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
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Qiu Y, Zhang J, Tong YW, He Y. Reverse electron transfer: Novel anaerobic methanogenesis pathway regulated through exogenous CO 2 synergized with biochar. BIORESOURCE TECHNOLOGY 2024; 401:130741. [PMID: 38670292 DOI: 10.1016/j.biortech.2024.130741] [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: 02/03/2024] [Revised: 03/25/2024] [Accepted: 04/24/2024] [Indexed: 04/28/2024]
Abstract
Acid accumulation and carbon emission are two major challenges in anaerobic digestion. Syntrophic consortia can employ reverse electron transfer (RET) to facilitate thermodynamically unfavorable redox reactions during acetogenesis. However, the potential mechanisms and regulatory methods of RET remain unclear. This study examines the regulatory mechanisms by which exogenous CO2 affects RET and demonstrates that biochar maximizes CO2 solubility at 25.8 mmol/L to enhance effects further. CO2 synergized with biochar significantly increases cumulative methane production and propionate degradation rate. From the bioenergetic perspective, CO2 decreases energy level to a maximum of -87 kJ/mol, strengthening the thermodynamic viability. The underlying mechanism can be attributed to RET promotion, as indicated by increased formate dehydrogenase and enrichment of H2/formate-producing bacteria with their partner Methanospirillum hungatei. Moreover, the 5 % 13CH4 and methane contribution result show that CO2 accomplishes directed methanogenesis. Overall, this investigation riches the roles of CO2 and biochar in AD surrounding RET.
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Affiliation(s)
- Yang Qiu
- China-UK Low Carbon College, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jingxin Zhang
- China-UK Low Carbon College, Shanghai Jiao Tong University, Shanghai 200240, China; School of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai 200240, China; Energy and Environmental Sustainability Solutions for Megacities (E2S2) Phase II, Campus for Research Excellence and Technological Enterprise (CREATE), 1 CREATE Way, Singapore, 138602, Singapore.
| | - Yen Wah Tong
- Department of Chemical & Biomolecular Engineering, National University of Singapore, Singapore; Energy and Environmental Sustainability Solutions for Megacities (E2S2) Phase II, Campus for Research Excellence and Technological Enterprise (CREATE), 1 CREATE Way, Singapore, 138602, Singapore
| | - Yiliang He
- China-UK Low Carbon College, Shanghai Jiao Tong University, Shanghai 200240, China; School of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
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Mitchell JH, Freedman AH, Delaney JA, Girguis PR. Co-expression analysis reveals distinct alliances around two carbon fixation pathways in hydrothermal vent symbionts. Nat Microbiol 2024; 9:1526-1539. [PMID: 38839975 DOI: 10.1038/s41564-024-01704-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Accepted: 04/19/2024] [Indexed: 06/07/2024]
Abstract
Most autotrophic organisms possess a single carbon fixation pathway. The chemoautotrophic symbionts of the hydrothermal vent tubeworm Riftia pachyptila, however, possess two functional pathways: the Calvin-Benson-Bassham (CBB) and the reductive tricarboxylic acid (rTCA) cycles. How these two pathways are coordinated is unknown. Here we measured net carbon fixation rates, transcriptional/metabolic responses and transcriptional co-expression patterns of Riftia pachyptila endosymbionts by incubating tubeworms collected from the East Pacific Rise at environmental pressures, temperature and geochemistry. Results showed that rTCA and CBB transcriptional patterns varied in response to different geochemical regimes and that each pathway is allied to specific metabolic processes; the rTCA is allied to hydrogenases and dissimilatory nitrate reduction, whereas the CBB is allied to sulfide oxidation and assimilatory nitrate reduction, suggesting distinctive yet complementary roles in metabolic function. Furthermore, our network analysis implicates the rTCA and a group 1e hydrogenase as key players in the physiological response to limitation of sulfide and oxygen. Net carbon fixation rates were also exemplary, and accordingly, we propose that co-activity of CBB and rTCA may be an adaptation for maintaining high carbon fixation rates, conferring a fitness advantage in dynamic vent environments.
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Coskun ÖK, Gomez-Saez GV, Beren M, Özcan D, Günay SD, Elkin V, Hoşgörmez H, Einsiedl F, Eisenreich W, Orsi WD. Quantifying genome-specific carbon fixation in a 750-meter deep subsurface hydrothermal microbial community. FEMS Microbiol Ecol 2024; 100:fiae062. [PMID: 38632042 DOI: 10.1093/femsec/fiae062] [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: 11/13/2023] [Revised: 02/16/2024] [Accepted: 04/16/2024] [Indexed: 04/19/2024] Open
Abstract
Dissolved inorganic carbon has been hypothesized to stimulate microbial chemoautotrophic activity as a biological sink in the carbon cycle of deep subsurface environments. Here, we tested this hypothesis using quantitative DNA stable isotope probing of metagenome-assembled genomes (MAGs) at multiple 13C-labeled bicarbonate concentrations in hydrothermal fluids from a 750-m deep subsurface aquifer in the Biga Peninsula (Turkey). The diversity of microbial populations assimilating 13C-labeled bicarbonate was significantly different at higher bicarbonate concentrations, and could be linked to four separate carbon-fixation pathways encoded within 13C-labeled MAGs. Microbial populations encoding the Calvin-Benson-Bassham cycle had the highest contribution to carbon fixation across all bicarbonate concentrations tested, spanning 1-10 mM. However, out of all the active carbon-fixation pathways detected, MAGs affiliated with the phylum Aquificae encoding the reverse tricarboxylic acid (rTCA) pathway were the only microbial populations that exhibited an increased 13C-bicarbonate assimilation under increasing bicarbonate concentrations. Our study provides the first experimental data supporting predictions that increased bicarbonate concentrations may promote chemoautotrophy via the rTCA cycle and its biological sink for deep subsurface inorganic carbon.
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Affiliation(s)
- Ömer K Coskun
- Department of Earth and Environmental Sciences, Ludwig-Maximilians-Universität, Richard-Wagner Straße 10, 80333 Munich, Germany
| | - Gonzalo V Gomez-Saez
- Department of Earth and Environmental Sciences, Ludwig-Maximilians-Universität, Richard-Wagner Straße 10, 80333 Munich, Germany
- GeoBio-Center, Ludwig-Maximilians-Universität München, Richard-Wagner Straße 10, 80333 Munich, Germany
| | - Murat Beren
- Department of Geological Engineering, Istanbul University - Cerrahpasa, Büyükçekmece Campus, Block G, Floor 5, Istanbul, Turkey
| | - Doğacan Özcan
- Department of Geological Engineering, Istanbul University - Cerrahpasa, Büyükçekmece Campus, Block G, Floor 5, Istanbul, Turkey
| | - Suna D Günay
- Department of Earth and Environmental Sciences, Ludwig-Maximilians-Universität, Richard-Wagner Straße 10, 80333 Munich, Germany
| | - Viktor Elkin
- Department of Earth and Environmental Sciences, Ludwig-Maximilians-Universität, Richard-Wagner Straße 10, 80333 Munich, Germany
| | - Hakan Hoşgörmez
- Department of Geological Engineering, Istanbul University - Cerrahpasa, Büyükçekmece Campus, Block G, Floor 5, Istanbul, Turkey
| | - Florian Einsiedl
- Chair of Hydrogeology, School of Engineering and Design, Technical University Munich, Arcisstraße 21, 80333 Munich, Germany
| | - Wolfgang Eisenreich
- Lehrstuhl für Biochemie, Department Chemie, Technische Universität München, Lichtenbergstraße, 85748 Garching, Germany
| | - William D Orsi
- Department of Earth and Environmental Sciences, Ludwig-Maximilians-Universität, Richard-Wagner Straße 10, 80333 Munich, Germany
- GeoBio-Center, Ludwig-Maximilians-Universität München, Richard-Wagner Straße 10, 80333 Munich, Germany
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Schulz-Mirbach H, Dronsella B, He H, Erb TJ. Creating new-to-nature carbon fixation: A guide. Metab Eng 2024; 82:12-28. [PMID: 38160747 DOI: 10.1016/j.ymben.2023.12.012] [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: 10/10/2023] [Revised: 12/23/2023] [Accepted: 12/27/2023] [Indexed: 01/03/2024]
Abstract
Synthetic biology aims at designing new biological functions from first principles. These new designs allow to expand the natural solution space and overcome the limitations of naturally evolved systems. One example is synthetic CO2-fixation pathways that promise to provide more efficient ways for the capture and conversion of CO2 than natural pathways, such as the Calvin Benson Bassham (CBB) cycle of photosynthesis. In this review, we provide a practical guideline for the design and realization of such new-to-nature CO2-fixation pathways. We introduce the concept of "synthetic CO2-fixation", and give a general overview over the enzymology and topology of synthetic pathways, before we derive general principles for their design from their eight naturally evolved analogs. We provide a comprehensive summary of synthetic carbon-assimilation pathways and derive a step-by-step, practical guide from the theoretical design to their practical implementation, before ending with an outlook on new developments in the field.
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Affiliation(s)
- Helena Schulz-Mirbach
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, 35043, Marburg, Germany
| | - Beau Dronsella
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, 35043, Marburg, Germany; Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam, Germany
| | - Hai He
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, 35043, Marburg, Germany
| | - Tobias J Erb
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, 35043, Marburg, Germany; Center for Synthetic Microbiology (SYNMIKRO), Karl-von-Frisch-Str. 16, D-35043, Marburg, Germany.
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Li H, Han Y, Zhang Y, Mi X, Wang D, Xu Y, Dong K. Optimization of nitrogen removal and microbial mechanism of a hydrogen-based membrane biofilm reactor. ENVIRONMENTAL TECHNOLOGY 2024:1-17. [PMID: 38362607 DOI: 10.1080/09593330.2024.2317817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 02/02/2024] [Indexed: 02/17/2024]
Abstract
The hydrogen-based membrane biofilm reactor (H2-MBfR) is an emerging biological nitrogen removal technology characterized by high efficiency, energy-saving capability, and environmental friendliness. The technology achieves denitrification and denitrogenation of microorganisms by passing hydrogen as an electron donor from inside to outside through the hollow fibre membrane module, and eventually the hydrogen reachs the biofilm attached to the surface of the fibre membrane. H2-MBfR has obtained favourable outcomes in the treatment of secondary biochemical effluent and low concentration nitrogen polluted water source. The experiment was optimized by s single-factor testing and response surface methodology-based optimization (RSM), and the optimal operational conditions were obtained as follows: an influent flow rate of 2 mL/min, hydrogen pressure of 0.04 MPa, and influent nitrate concentration of 24.29 mg/L. Under these conditions, a high nitrate removal rate of 98.25% was achieved. In addition, Proteobacteria and Bacteroidetes were the dominant bacteria in all stages, and the genus Hydrogenophaga was sufficiently enriched, occurring at 13.0%-49.0% throughout the reactor operation. Furthermore, the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway for nitrate reduction and inorganic carbon utilization by microorganisms in the H2-MBfR was explored through comparison with the KEGG database. The results provided a mechanistic explanation for the denitrification and carbon sequestration capacity of the H2-MBfR.
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Affiliation(s)
- Haixiang Li
- College of Environmental Science and Engineering, Guilin University of Technology, Guilin, People's Republic of China
- The Guangxi Key Laboratory of Theory and Technology for Environmental Pollution Control, Guilin, People's Republic of China
| | - Yu Han
- College of Environmental Science and Engineering, Guilin University of Technology, Guilin, People's Republic of China
| | - Yanhao Zhang
- College of Municipal and Environmental Engineering, Shandong Jianzhu University, Jinan, People's Republic of China
| | - Xiaojuan Mi
- College of Engineering, Jilin Normal University, Siping, People's Republic of China
| | - Dunqiu Wang
- College of Environmental Science and Engineering, Guilin University of Technology, Guilin, People's Republic of China
| | - Yufeng Xu
- College of Environmental Science and Engineering, Guilin University of Technology, Guilin, People's Republic of China
- The Guangxi Key Laboratory of Theory and Technology for Environmental Pollution Control, Guilin, People's Republic of China
| | - Kun Dong
- College of Environmental Science and Engineering, Guilin University of Technology, Guilin, People's Republic of China
- The Guangxi Key Laboratory of Theory and Technology for Environmental Pollution Control, Guilin, People's Republic of China
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Zhang J, Li F, Liu D, Liu Q, Song H. Engineering extracellular electron transfer pathways of electroactive microorganisms by synthetic biology for energy and chemicals production. Chem Soc Rev 2024; 53:1375-1446. [PMID: 38117181 DOI: 10.1039/d3cs00537b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2023]
Abstract
The excessive consumption of fossil fuels causes massive emission of CO2, leading to climate deterioration and environmental pollution. The development of substitutes and sustainable energy sources to replace fossil fuels has become a worldwide priority. Bio-electrochemical systems (BESs), employing redox reactions of electroactive microorganisms (EAMs) on electrodes to achieve a meritorious combination of biocatalysis and electrocatalysis, provide a green and sustainable alternative approach for bioremediation, CO2 fixation, and energy and chemicals production. EAMs, including exoelectrogens and electrotrophs, perform extracellular electron transfer (EET) (i.e., outward and inward EET), respectively, to exchange energy with the environment, whose rate determines the efficiency and performance of BESs. Therefore, we review the synthetic biology strategies developed in the last decade for engineering EAMs to enhance the EET rate in cell-electrode interfaces for facilitating the production of electricity energy and value-added chemicals, which include (1) progress in genetic manipulation and editing tools to achieve the efficient regulation of gene expression, knockout, and knockdown of EAMs; (2) synthetic biological engineering strategies to enhance the outward EET of exoelectrogens to anodes for electricity power production and anodic electro-fermentation (AEF) for chemicals production, including (i) broadening and strengthening substrate utilization, (ii) increasing the intracellular releasable reducing equivalents, (iii) optimizing c-type cytochrome (c-Cyts) expression and maturation, (iv) enhancing conductive nanowire biosynthesis and modification, (v) promoting electron shuttle biosynthesis, secretion, and immobilization, (vi) engineering global regulators to promote EET rate, (vii) facilitating biofilm formation, and (viii) constructing cell-material hybrids; (3) the mechanisms of inward EET, CO2 fixation pathway, and engineering strategies for improving the inward EET of electrotrophic cells for CO2 reduction and chemical production, including (i) programming metabolic pathways of electrotrophs, (ii) rewiring bioelectrical circuits for enhancing inward EET, and (iii) constructing microbial (photo)electrosynthesis by cell-material hybridization; (4) perspectives on future challenges and opportunities for engineering EET to develop highly efficient BESs for sustainable energy and chemical production. We expect that this review will provide a theoretical basis for the future development of BESs in energy harvesting, CO2 fixation, and chemical synthesis.
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Affiliation(s)
- Junqi Zhang
- Frontier Science Center for Synthetic Biology (Ministry of Education), Key Laboratory of Systems Bioengineering, and School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China.
| | - Feng Li
- Frontier Science Center for Synthetic Biology (Ministry of Education), Key Laboratory of Systems Bioengineering, and School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China.
| | - Dingyuan Liu
- Frontier Science Center for Synthetic Biology (Ministry of Education), Key Laboratory of Systems Bioengineering, and School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China.
| | - Qijing Liu
- Frontier Science Center for Synthetic Biology (Ministry of Education), Key Laboratory of Systems Bioengineering, and School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China.
| | - Hao Song
- Frontier Science Center for Synthetic Biology (Ministry of Education), Key Laboratory of Systems Bioengineering, and School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China.
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Wu H, Cui H, Fu C, Li R, Qi F, Liu Z, Yang G, Xiao K, Qiao M. Unveiling the crucial role of soil microorganisms in carbon cycling: A review. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 909:168627. [PMID: 37977383 DOI: 10.1016/j.scitotenv.2023.168627] [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: 09/25/2023] [Revised: 11/13/2023] [Accepted: 11/14/2023] [Indexed: 11/19/2023]
Abstract
Soil microorganisms, by actively participating in the decomposition and transformation of organic matter through diverse metabolic pathways, play a pivotal role in carbon cycling within soil systems and contribute to the stabilization of organic carbon, thereby influencing soil carbon storage and turnover. Investigating the processes, mechanisms, and driving factors of soil microbial carbon cycling is crucial for understanding the functionality of terrestrial carbon sinks and effectively addressing climate change. This review comprehensively discusses the role of soil microorganisms in soil carbon cycling from three perspectives: metabolic pathways, microbial communities, and environmental influences. It elucidates the roles of different microbial species in carbon cycling and highlights the impact of microbial interactions and environmental factors on carbon cycling. Through the synthesis of 2171 relevant papers in the Web of Science Core database, we elucidated the ecological community structure, activity, and assembly mechanisms of soil microorganisms crucial to the soil carbon cycle that have been widely analyzed. The integration of soil microbial carbon cycle and its driving factors are vital for accurately predicting and modeling biogeochemical cycles and effectively addressing the challenges posed by global climate change. Such integration is vital for accurately predicting and modeling biogeochemical cycles and effectively addressing the challenges posed by global climate change.
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Affiliation(s)
- Haowei Wu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Huiling Cui
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Chenxi Fu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Ran Li
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Fengyuan Qi
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Zhelun Liu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Guang Yang
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Keqing Xiao
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China.
| | - Min Qiao
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China.
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Yang X, Zhang Y, Zhao G. Artificial carbon assimilation: From unnatural reactions and pathways to synthetic autotrophic systems. Biotechnol Adv 2024; 70:108294. [PMID: 38013126 DOI: 10.1016/j.biotechadv.2023.108294] [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: 07/28/2023] [Revised: 10/26/2023] [Accepted: 11/18/2023] [Indexed: 11/29/2023]
Abstract
Synthetic biology is being increasingly used to establish novel carbon assimilation pathways and artificial autotrophic strains that can be used in low-carbon biomanufacturing. Currently, artificial pathway design has made significant progress from advocacy to practice within a relatively short span of just over ten years. However, there is still huge scope for exploration of pathway diversity, operational efficiency, and host suitability. The accelerated research process will bring greater opportunities and challenges. In this paper, we provide a comprehensive summary and interpretation of representative one-carbon assimilation pathway designs and artificial autotrophic strain construction work. In addition, we propose some feasible design solutions based on existing research results and patterns to promote the development and application of artificial autotrophy.
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Affiliation(s)
- Xue Yang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China; National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China; Haihe Laboratory of Synthetic Biology, Tianjin 300308, China
| | - Yanfei Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China; National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China.
| | - Guoping Zhao
- National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China; CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China.
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Fukuyama Y, Shimamura S, Sakai S, Michimori Y, Sumida T, Chikaraishi Y, Atomi H, Nunoura T. Development of a rapid and highly accurate method for 13C tracer-based metabolomics and its application on a hydrogenotrophic methanogen. ISME COMMUNICATIONS 2024; 4:ycad006. [PMID: 38282645 PMCID: PMC10809761 DOI: 10.1093/ismeco/ycad006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 11/24/2023] [Accepted: 12/01/2023] [Indexed: 01/30/2024]
Abstract
Microfluidic capillary electrophoresis-mass spectrometry (CE-MS) is a rapid and highly accurate method to determine isotopomer patterns in isotopically labeled compounds. Here, we developed a novel method for tracer-based metabolomics using CE-MS for underivatized proteinogenic amino acids. The method consisting of a ZipChip CE system and a high-resolution Orbitrap Fusion Tribrid mass spectrometer allows us to obtain highly accurate data from 1 μl of 100 nmol/l amino acids comparable to a mere 1 [Formula: see text] 104-105 prokaryotic cells. To validate the capability of the CE-MS method, we analyzed 16 protein-derived amino acids from a methanogenic archaeon Methanothermobacter thermautotrophicus as a model organism, and the mass spectra showed sharp peaks with low mass errors and background noise. Tracer-based metabolome analysis was then performed to identify the central carbon metabolism in M. thermautotrophicus using 13C-labeled substrates. The mass isotopomer distributions of serine, aspartate, and glutamate revealed the occurrence of both the Wood-Ljungdahl pathway and an incomplete reductive tricarboxylic acid cycle for carbon fixation. In addition, biosynthesis pathways of 15 amino acids were constructed based on the mass isotopomer distributions of the detected protein-derived amino acids, genomic information, and public databases. Among them, the presence of alternative enzymes of alanine dehydrogenase, ornithine cyclodeaminase, and homoserine kinase was suggested in the biosynthesis pathways of alanine, proline, and threonine, respectively. To our knowledge, the novel 13C tracer-based metabolomics using CE-MS can be considered the most efficient method to identify central carbon metabolism and amino acid biosynthesis pathways and is applicable to any kind of isolated microbe.
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Affiliation(s)
- Yuto Fukuyama
- Research Center for Bioscience and Nanoscience (CeBN), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2–15 Natsushima-cho, Yokosuka, Kanagawa 237–0061, Japan
| | - Shigeru Shimamura
- Institute for Extra-Cutting-Edge Science and Technology Avant-Garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2–15 Natsushima-cho, Yokosuka, Kanagawa 237–0061, Japan
| | - Sanae Sakai
- Institute for Extra-Cutting-Edge Science and Technology Avant-Garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2–15 Natsushima-cho, Yokosuka, Kanagawa 237–0061, Japan
| | - Yuta Michimori
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Tomomi Sumida
- Research Center for Bioscience and Nanoscience (CeBN), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2–15 Natsushima-cho, Yokosuka, Kanagawa 237–0061, Japan
| | - Yoshito Chikaraishi
- Institute of Low Temperature Science, Hokkaido University, Kita-19, Nishi-8, Kita-ku, Sapporo 060-0819, Japan
| | - Haruyuki Atomi
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Takuro Nunoura
- Research Center for Bioscience and Nanoscience (CeBN), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2–15 Natsushima-cho, Yokosuka, Kanagawa 237–0061, Japan
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11
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Shan S, Wang S, Yan X, Chen K, Liang L, Li X, Zhou C, Yan X, Ruan R, Cheng P. Mixotrophic culture of Chaetoceros sp. and the synergistic carbon and energy metabolism. BIORESOURCE TECHNOLOGY 2023; 390:129912. [PMID: 37879446 DOI: 10.1016/j.biortech.2023.129912] [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: 09/22/2023] [Revised: 10/20/2023] [Accepted: 10/21/2023] [Indexed: 10/27/2023]
Abstract
This research studied the metabolic mechanism of the mixotrophic Chaetoceros sp. The results showed this alga had the highest cell density and growth rate of 47.72 × 105 cells mL-1 and 0.41 d-1, respectively, with a maximum dry weight of 2.90 g/L, when compared to photoautotrophic and photoheterotrophic modes. Compared to photoheterotrophy, transcriptomics results showed the Rubisco, PGK, and GAPDH related genes were separately up-regulated by 1.03, 2.36, and 1.36 times in CBB cycle in mixotrophic mode, suggesting intermediate metabolites of EMP and PPP can enter the chloroplast via transporter proteins, or membrane permeation, and feedback inhibition regulates the reduction of multiple reactions in CBB cycle. Chaetoceros sp. achieves high biomass by utilizing ATP and carbon structures from EMP and PPP pathways, and the addition of NaHCO3 leads to an up-regulation of CBB cycle for the mixotrophic alga, resulting in higher biomass compared to the photoheterotrophic mode.
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Affiliation(s)
- Shengzhou Shan
- College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, Zhejiang 315211, China
| | - Shanshan Wang
- The First Affiliated Hospital of Ningbo University, Ningbo, Zhejiang 315211, China
| | - Xi Yan
- College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, Zhejiang 315211, China
| | - Kang Chen
- College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, Zhejiang 315211, China; Food Chemistry and Food Development, Department of Biochemistry, University of Turku, Turun yliopisto, Turku FI-20014, Finland
| | - Li Liang
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, 214122, China
| | - Xiaohui Li
- College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, Zhejiang 315211, China
| | - Chengxu Zhou
- College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, Zhejiang 315211, China
| | - Xiaojun Yan
- Key Laboratory of Marine Biotechnology of Zhejiang Province, Ningbo University, Ningbo, Zhejiang 315211, China
| | - Roger Ruan
- Center for Biorefining, and Department of Bioproducts and Biosystems Engineering, University of Minnesota-Twin Cities, Saint Paul, MN 55108, USA.
| | - Pengfei Cheng
- College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, Zhejiang 315211, China; Center for Biorefining, and Department of Bioproducts and Biosystems Engineering, University of Minnesota-Twin Cities, Saint Paul, MN 55108, USA.
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12
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Kang DK, Kim SH, Sohn JH, Sung BH. Insights into Enzyme Reactions with Redox Cofactors in Biological Conversion of CO 2. J Microbiol Biotechnol 2023; 33:1403-1411. [PMID: 37482811 DOI: 10.4014/jmb.2306.06005] [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: 06/05/2023] [Revised: 06/12/2023] [Accepted: 06/12/2023] [Indexed: 07/25/2023]
Abstract
Carbon dioxide (CO2) is the most abundant component of greenhouse gases (GHGs) and directly creates environmental issues such as global warming and climate change. Carbon capture and storage have been proposed mainly to solve the problem of increasing CO2 concentration in the atmosphere; however, more emphasis has recently been placed on its use. Among the many methods of using CO2, one of the key environmentally friendly technologies involves biologically converting CO2 into other organic substances such as biofuels, chemicals, and biomass via various metabolic pathways. Although an efficient biocatalyst for industrial applications has not yet been developed, biological CO2 conversion is the needed direction. To this end, this review briefly summarizes seven known natural CO2 fixation pathways according to carbon number and describes recent studies in which natural CO2 assimilation systems have been applied to heterogeneous in vivo and in vitro systems. In addition, studies on the production of methanol through the reduction of CO2 are introduced. The importance of redox cofactors, which are often overlooked in the CO2 assimilation reaction by enzymes, is presented; methods for their recycling are proposed. Although more research is needed, biological CO2 conversion will play an important role in reducing GHG emissions and producing useful substances in terms of resource cycling.
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Affiliation(s)
- Du-Kyeong Kang
- Synthetic Biology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
- Department of Biosystems and Bioengineering, Korea University of Science and Technology (UST), Daejeon 34113, Republic of Korea
| | - Seung-Hwa Kim
- Synthetic Biology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
- Department of Biosystems and Bioengineering, Korea University of Science and Technology (UST), Daejeon 34113, Republic of Korea
| | - Jung-Hoon Sohn
- Synthetic Biology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
- Department of Biosystems and Bioengineering, Korea University of Science and Technology (UST), Daejeon 34113, Republic of Korea
| | - Bong Hyun Sung
- Synthetic Biology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
- Department of Biosystems and Bioengineering, Korea University of Science and Technology (UST), Daejeon 34113, Republic of Korea
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13
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Bährle R, Böhnke S, Englhard J, Bachmann J, Perner M. Current status of carbon monoxide dehydrogenases (CODH) and their potential for electrochemical applications. BIORESOUR BIOPROCESS 2023; 10:84. [PMID: 38647803 PMCID: PMC10992861 DOI: 10.1186/s40643-023-00705-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 11/16/2023] [Indexed: 04/25/2024] Open
Abstract
Anthropogenic carbon dioxide (CO2) levels are rising to alarming concentrations in earth's atmosphere, causing adverse effects and global climate changes. In the last century, innovative research on CO2 reduction using chemical, photochemical, electrochemical and enzymatic approaches has been addressed. In particular, natural CO2 conversion serves as a model for many processes and extensive studies on microbes and enzymes regarding redox reactions involving CO2 have already been conducted. In this review we focus on the enzymatic conversion of CO2 to carbon monoxide (CO) as the chemical conversion downstream of CO production render CO particularly attractive as a key intermediate. We briefly discuss the different currently known natural autotrophic CO2 fixation pathways, focusing on the reversible reaction of CO2, two electrons and protons to CO and water, catalyzed by carbon monoxide dehydrogenases (CODHs). We then move on to classify the different type of CODHs, involved catalyzed chemical reactions and coupled metabolisms. Finally, we discuss applications of CODH enzymes in photochemical and electrochemical cells to harness CO2 from the environment transforming it into commodity chemicals.
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Affiliation(s)
- Rebecca Bährle
- Department of Marine Geomicrobiology, Faculty of Marine Biogeochemistry, GEOMAR Helmholtz Centre for Ocean Research Kiel, Wischhofstr. 1-3, 24148, Kiel, Germany
| | - Stefanie Böhnke
- Department of Marine Geomicrobiology, Faculty of Marine Biogeochemistry, GEOMAR Helmholtz Centre for Ocean Research Kiel, Wischhofstr. 1-3, 24148, Kiel, Germany
| | - Jonas Englhard
- Chemistry of Thin Film Materials, IZNF, Friedrich-Alexander-Universität Erlangen-Nürnberg, Cauerstr. 3, 91058, Erlangen, Germany
| | - Julien Bachmann
- Chemistry of Thin Film Materials, IZNF, Friedrich-Alexander-Universität Erlangen-Nürnberg, Cauerstr. 3, 91058, Erlangen, Germany
| | - Mirjam Perner
- Department of Marine Geomicrobiology, Faculty of Marine Biogeochemistry, GEOMAR Helmholtz Centre for Ocean Research Kiel, Wischhofstr. 1-3, 24148, Kiel, Germany.
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14
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Mrnjavac N, Wimmer JLE, Brabender M, Schwander L, Martin WF. The Moon-Forming Impact and the Autotrophic Origin of Life. Chempluschem 2023; 88:e202300270. [PMID: 37812146 PMCID: PMC7615287 DOI: 10.1002/cplu.202300270] [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: 06/05/2023] [Revised: 09/29/2023] [Accepted: 10/03/2023] [Indexed: 10/10/2023]
Abstract
The Moon-forming impact vaporized part of Earth's mantle, and turned the rest into a magma ocean, from which carbon dioxide degassed into the atmosphere, where it stayed until water rained out to form the oceans. The rain dissolved CO2 and made it available to react with transition metal catalysts in the Earth's crust so as to ultimately generate the organic compounds that form the backbone of microbial metabolism. The Moon-forming impact was key in building a planet with the capacity to generate life in that it converted carbon on Earth into a homogeneous and accessible substrate for organic synthesis. Today all ecosystems, without exception, depend upon primary producers, organisms that fix CO2 . According to theories of autotrophic origin, it has always been that way, because autotrophic theories posit that the first forms of life generated all the molecules needed to build a cell from CO2 , forging a direct line of continuity between Earth's initial CO2 -rich atmosphere and the first microorganisms. By modern accounts these were chemolithoautotrophic archaea and bacteria that initially colonized the crust and still inhabit that environment today.
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Affiliation(s)
- Natalia Mrnjavac
- Department of Biology Institute for Molecular Evolution Heinrich Heine University Duesseldorf Universitaetsstr. 1, 40225 Düsseldorf (Germany)
| | - Jessica L. E. Wimmer
- Department of Biology Institute for Molecular Evolution Heinrich Heine University Duesseldorf Universitaetsstr. 1, 40225 Düsseldorf (Germany)
| | - Max Brabender
- Department of Biology Institute for Molecular Evolution Heinrich Heine University Duesseldorf Universitaetsstr. 1, 40225 Düsseldorf (Germany)
| | - Loraine Schwander
- Department of Biology Institute for Molecular Evolution Heinrich Heine University Duesseldorf Universitaetsstr. 1, 40225 Düsseldorf (Germany)
| | - William F. Martin
- Department of Biology Institute for Molecular Evolution Heinrich Heine University Duesseldorf Universitaetsstr. 1, 40225 Düsseldorf (Germany)
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15
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Pavlova ON, Tupikin AE, Chernitsyna SM, Bukin YS, Lomakina AV, Pogodaeva TV, Nikonova AA, Bukin SV, Zemskaya TI, Kabilov MR. Description and Genomic Analysis of the First Facultatively Lithoautotrophic, Thermophilic Bacteria of the Genus Thermaerobacter Isolated from Low-temperature Sediments of Lake Baikal. MICROBIAL ECOLOGY 2023; 86:1604-1619. [PMID: 36717392 DOI: 10.1007/s00248-023-02182-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Accepted: 01/19/2023] [Indexed: 06/18/2023]
Abstract
Members of the genus Thermaerobacter belong to the phylum Firmicutes and all isolates characterised to date are strictly aerobic and thermophilic. They were isolated from a mud sample of the Challenger Deep in the Mariana Trench, hydrothermal vents, and silt compost. A novel thermophilic, facultatively lithoautotrophic bacteria of the genus Thermaerobacter, strain PB12/4term (=VKM B-3151T), with a metabolism that is uncharacteristic of the type species, was isolated from low-temperature surface sediments near the Posolsk Bank methane seep, Lake Baikal, Russia. The new strain grows with molecular hydrogen as electron donor, elemental sulfur, and thiosulfate as electron acceptors, and CO2/[Formula: see text] as carbon source. The genome of strain PB12/4term consists of one chromosome with a total length of 2.820.915 bp and the G+C content of the genomic DNA was 72.2%. The phylogenomic reconstruction based on 120 conserved bacterial single-copy proteins revealed that strain PB12/4term belongs to the genus Thermaerobacter within in the class Thermaerobacteria, phylum Firmicutes_E. The strain PB12/4term is closely related to Thermaerobacter subterraneus DSM 13965 (ANI=95.08%, AF=0.91) and Thermaerobacter marianensis DSM 12885 (ANI=84.98%, AF=0.77). Genomic and experimental data confirm the ability of the Thermaerobacter PB12/4term pure culture to facultatively lithotrophic growth, which is provided by the presence of [NiFe]hydrogenase enzymes that are absent in T. marianensis DSM 12885 and T. subterraneus DSM 13965. The data obtained on the physiological and biochemical differences of strain PB12/4term provide a deeper insight into the species diversity and functional activity of the genus Thermaerobacter.
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Affiliation(s)
- O N Pavlova
- Laboratory of Hydrocarbon Microbiology, Limnological Institute, Siberian Branch, Russian Academy of Sciences, Irkutsk, Russia.
| | - A E Tupikin
- SB RAS Genomics Core Facility, Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia
| | - S M Chernitsyna
- Laboratory of Hydrocarbon Microbiology, Limnological Institute, Siberian Branch, Russian Academy of Sciences, Irkutsk, Russia
| | - Y S Bukin
- Laboratory of Genosystematics, Limnological Institute, Siberian Branch, Russian Academy of Sciences, Irkutsk, Russia
| | - A V Lomakina
- Laboratory of Hydrocarbon Microbiology, Limnological Institute, Siberian Branch, Russian Academy of Sciences, Irkutsk, Russia
| | - T V Pogodaeva
- Laboratory of Hydrochemistry and Atmosphere Chemistry, Limnological Institute, Siberian Branch, Russian Academy of Sciences, Irkutsk, Russia
| | - A A Nikonova
- Laboratory of Chromatography, Limnological Institute, Siberian Branch, Russian Academy of Sciences, Irkutsk, Russia
| | - S V Bukin
- Laboratory of Hydrocarbon Microbiology, Limnological Institute, Siberian Branch, Russian Academy of Sciences, Irkutsk, Russia
| | - T I Zemskaya
- Laboratory of Hydrocarbon Microbiology, Limnological Institute, Siberian Branch, Russian Academy of Sciences, Irkutsk, Russia
| | - M R Kabilov
- SB RAS Genomics Core Facility, Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia
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16
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Balbay MG, Shlafstein MD, Cockell C, Cady SL, Prescott RD, Lim DSS, Chain PSG, Donachie SP, Decho AW, Saw JH. Metabolic versatility of Caldarchaeales from geothermal features of Hawai'i and Chile as revealed by five metagenome-assembled genomes. Front Microbiol 2023; 14:1216591. [PMID: 37799600 PMCID: PMC10547907 DOI: 10.3389/fmicb.2023.1216591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 08/30/2023] [Indexed: 10/07/2023] Open
Abstract
Members of the archaeal order Caldarchaeales (previously the phylum Aigarchaeota) are poorly sampled and are represented in public databases by relatively few genomes. Additional representative genomes will help resolve their placement among all known members of Archaea and provide insights into their roles in the environment. In this study, we analyzed 16S rRNA gene amplicons belonging to the Caldarchaeales that are available in public databases, which demonstrated that archaea of the order Caldarchaeales are diverse, widespread, and most abundant in geothermal habitats. We also constructed five metagenome-assembled genomes (MAGs) of Caldarchaeales from two geothermal features to investigate their metabolic potential and phylogenomic position in the domain Archaea. Two of the MAGs were assembled from microbial community DNA extracted from fumarolic lava rocks from Mauna Ulu, Hawai'i, and three were assembled from DNA obtained from hot spring sinters from the El Tatio geothermal field in Chile. MAGs from Hawai'i are high quality bins with completeness >95% and contamination <1%, and one likely belongs to a novel species in a new genus recently discovered at a submarine volcano off New Zealand. MAGs from Chile have lower completeness levels ranging from 27 to 70%. Gene content of the MAGs revealed that these members of Caldarchaeales are likely metabolically versatile and exhibit the potential for both chemoorganotrophic and chemolithotrophic lifestyles. The wide array of metabolic capabilities exhibited by these members of Caldarchaeales might help them thrive under diverse harsh environmental conditions. All the MAGs except one from Chile harbor putative prophage regions encoding several auxiliary metabolic genes (AMGs) that may confer a fitness advantage on their Caldarchaeales hosts by increasing their metabolic potential and make them better adapted to new environmental conditions. Phylogenomic analysis of the five MAGs and over 3,000 representative archaeal genomes showed the order Caldarchaeales forms a monophyletic group that is sister to the clade comprising the orders Geothermarchaeales (previously Candidatus Geothermarchaeota), Conexivisphaerales and Nitrososphaerales (formerly known as Thaumarchaeota), supporting the status of Caldarchaeales members as a clade distinct from the Thaumarchaeota.
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Affiliation(s)
- Manolya Gul Balbay
- Department of Biological Sciences, The George Washington University, Washington, DC, United States
| | | | - Charles Cockell
- UK Centre for Astrobiology, University of Edinburgh, Edinburgh, United Kingdom
| | - Sherry L. Cady
- Department of Geology, Portland State University, Portland, OR, United States
| | - Rebecca D. Prescott
- UK Centre for Astrobiology, University of Edinburgh, Edinburgh, United Kingdom
- School of Life Sciences, University of Hawai’i at Mānoa, Honolulu, HI, United States
- Department of Environmental Health Sciences, University of South Carolina, Columbia, SC, United States
- Department of Biology, University of Mississippi, Oxford, MS, United States
| | | | | | - Stuart P. Donachie
- School of Life Sciences, University of Hawai’i at Mānoa, Honolulu, HI, United States
| | - Alan W. Decho
- Department of Environmental Health Sciences, University of South Carolina, Columbia, SC, United States
| | - Jimmy H. Saw
- Department of Biological Sciences, The George Washington University, Washington, DC, United States
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17
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Penumutchu S, Korry BJ, Hewlett K, Belenky P. Fiber supplementation protects from antibiotic-induced gut microbiome dysbiosis by modulating gut redox potential. Nat Commun 2023; 14:5161. [PMID: 37620319 PMCID: PMC10449846 DOI: 10.1038/s41467-023-40553-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 07/31/2023] [Indexed: 08/26/2023] Open
Abstract
Antibiotic-induced gut dysbiosis (AID) is a frequent and serious side effect of antibiotic use and mitigating this dysbiosis is a critical therapeutic target. We propose that the host diet can modulate the chemical environment of the gut resulting in changes to the structure and function of the microbiome during antibiotic treatment. Gut dysbiosis is typically characterized by increases in aerobic respiratory bacterial metabolism, redox potential, and abundance of Proteobacteria. In this study, we explore dietary fiber supplements as potential modulators of the chemical environment in the gut to reduce this pattern of dysbiosis. Using defined-diets and whole-genome sequencing of female murine microbiomes during diet modulation and antibiotic treatment, we find that fiber prebiotics significantly reduced the impact of antibiotic treatment on microbiome composition and function. We observe reduced abundance of aerobic bacteria as well as metabolic pathways associated with oxidative metabolism. These metatranscriptomic results are corroborated by chemical measurements of eH and pH suggesting that fiber dampens the dysbiotic effects of antibiotics. This work indicates that fiber may act as a potential therapeutic for AID by modulating bacterial metabolism in the gut to prevent an increase in redox potential and protect commensal microbes during antibiotic treatment.
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Affiliation(s)
- Swathi Penumutchu
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI, 02912, USA
| | - Benjamin J Korry
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI, 02912, USA
| | - Katharine Hewlett
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Peter Belenky
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI, 02912, USA.
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18
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Bi H, Xu C, Bao Y, Zhang C, Wang K, Zhang Y, Wang M, Chen B, Fang Y, Tan T. Enhancing precursor supply and modulating metabolism to achieve high-level production of β-farnesene in Yarrowia lipolytica. BIORESOURCE TECHNOLOGY 2023; 382:129171. [PMID: 37196740 DOI: 10.1016/j.biortech.2023.129171] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 05/09/2023] [Accepted: 05/11/2023] [Indexed: 05/19/2023]
Abstract
β-Farnesene is a sesquiterpene commonly found in essential oils of plants, with applications spanning from agricultural pest control and biofuels to industrial chemicals. The use of renewable substrates in microbial cell factories offers a sustainable approach to β-farnesene biosynthesis. In this study, malic enzyme from Mucor circinelloides was examined for NADPH regeneration, concomitant with the augmentation of cytosolic acetyl-CoA supply by expressing ATP-citrate lyase from Mus musculus and manipulating the citrate pathway via AMP deaminase and isocitrate dehydrogenase. Carbon flux was modulated through the elimination of native 6-phosphofructokinase, while the incorporation of an exogenous non-oxidative glycolysis pathway served to bridge the pentose phosphate pathway with the mevalonate pathway. The resulting orthogonal precursor supply pathway facilitated β-farnesene production, reaching 810 mg/L in shake-flask fermentation. Employing optimal fermentation conditions and feeding strategy, a titer of 28.9 g/L of β-farnesene was attained in a 2 L bioreactor.
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Affiliation(s)
- Haoran Bi
- National Energy R&D Center of Biorefinery, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, P.R. China
| | - Chenchen Xu
- National Energy R&D Center of Biorefinery, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, P.R. China
| | - Yufei Bao
- National Energy R&D Center of Biorefinery, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, P.R. China
| | - Changwei Zhang
- National Energy R&D Center of Biorefinery, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, P.R. China
| | - Kai Wang
- National Energy R&D Center of Biorefinery, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, P.R. China
| | - Yang Zhang
- National Energy R&D Center of Biorefinery, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, P.R. China
| | - Meng Wang
- National Energy R&D Center of Biorefinery, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, P.R. China.
| | - Biqiang Chen
- National Energy R&D Center of Biorefinery, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, P.R. China
| | - Yunming Fang
- National Energy R&D Center of Biorefinery, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, P.R. China
| | - Tianwei Tan
- National Energy R&D Center of Biorefinery, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, P.R. China.
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19
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Sharko A, Spitzbarth B, Hermans TM, Eelkema R. Redox-Controlled Shunts in a Synthetic Chemical Reaction Cycle. J Am Chem Soc 2023; 145:9672-9678. [PMID: 37092741 PMCID: PMC10161229 DOI: 10.1021/jacs.3c00985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
Shunts, alternative pathways in chemical reaction networks (CRNs), are ubiquitous in nature, enabling adaptability to external and internal stimuli. We introduce a CRN in which the recovery of Michael-accepting species is driven by oxidation chemistry. Using weak oxidants can enable access to two shunts within this CRN with different kinetics and a reduced number of side reactions compared to the main cycle that is driven by strong oxidants. Furthermore, we introduce a strategy to recycle one of the main products under flow conditions to partially reverse the CRN and control product speciation throughout time. These findings introduce new levels of control over artificial CRNs, driven by redox chemistry, narrowing the gap between synthetic and natural systems.
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Affiliation(s)
| | - Benjamin Spitzbarth
- Department of Chemical Engineering, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Thomas M Hermans
- University of Strasbourg & CNRS, UMR7140, 67083 Strasbourg, France
| | - Rienk Eelkema
- Department of Chemical Engineering, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
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20
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Chu N, Jiang Y, Liang Q, Liu P, Wang D, Chen X, Li D, Liang P, Zeng RJ, Zhang Y. Electricity-Driven Microbial Metabolism of Carbon and Nitrogen: A Waste-to-Resource Solution. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:4379-4395. [PMID: 36877891 DOI: 10.1021/acs.est.2c07588] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Electricity-driven microbial metabolism relies on the extracellular electron transfer (EET) process between microbes and electrodes and provides promise for resource recovery from wastewater and industrial discharges. Over the past decades, tremendous efforts have been dedicated to designing electrocatalysts and microbes, as well as hybrid systems to push this approach toward industrial adoption. This paper summarizes these advances in order to facilitate a better understanding of electricity-driven microbial metabolism as a sustainable waste-to-resource solution. Quantitative comparisons of microbial electrosynthesis and abiotic electrosynthesis are made, and the strategy of electrocatalyst-assisted microbial electrosynthesis is critically discussed. Nitrogen recovery processes including microbial electrochemical N2 fixation, electrocatalytic N2 reduction, dissimilatory nitrate reduction to ammonium (DNRA), and abiotic electrochemical nitrate reduction to ammonia (Abio-NRA) are systematically reviewed. Furthermore, the synchronous metabolism of carbon and nitrogen using hybrid inorganic-biological systems is discussed, including advanced physicochemical, microbial, and electrochemical characterizations involved in this field. Finally, perspectives for future trends are presented. The paper provides valuable insights on the potential contribution of electricity-driven microbial valorization of waste carbon and nitrogen toward a green and sustainable society.
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Affiliation(s)
- Na Chu
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- CAS Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yong Jiang
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Qinjun Liang
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Panpan Liu
- School of Ecology and Environment, Zhengzhou University, Zhengzhou 450001, China
| | - Donglin Wang
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Xueming Chen
- Fujian Provincial Engineering Research Center of Rural Waste Recycling Technology, College of Environment and Safety Engineering, Fuzhou University, Fuzhou 350116, China
| | - Daping Li
- CAS Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
| | - Peng Liang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, PR China
| | - Raymond Jianxiong Zeng
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yifeng Zhang
- Department of Environmental Engineering, Technical University of Denmark, DK-2800 Lyngby, Denmark
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21
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Bierbaumer S, Nattermann M, Schulz L, Zschoche R, Erb TJ, Winkler CK, Tinzl M, Glueck SM. Enzymatic Conversion of CO 2: From Natural to Artificial Utilization. Chem Rev 2023; 123:5702-5754. [PMID: 36692850 PMCID: PMC10176493 DOI: 10.1021/acs.chemrev.2c00581] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Enzymatic carbon dioxide fixation is one of the most important metabolic reactions as it allows the capture of inorganic carbon from the atmosphere and its conversion into organic biomass. However, due to the often unfavorable thermodynamics and the difficulties associated with the utilization of CO2, a gaseous substrate that is found in comparatively low concentrations in the atmosphere, such reactions remain challenging for biotechnological applications. Nature has tackled these problems by evolution of dedicated CO2-fixing enzymes, i.e., carboxylases, and embedding them in complex metabolic pathways. Biotechnology employs such carboxylating and decarboxylating enzymes for the carboxylation of aromatic and aliphatic substrates either by embedding them into more complex reaction cascades or by shifting the reaction equilibrium via reaction engineering. This review aims to provide an overview of natural CO2-fixing enzymes and their mechanistic similarities. We also discuss biocatalytic applications of carboxylases and decarboxylases for the synthesis of valuable products and provide a separate summary of strategies to improve the efficiency of such processes. We briefly summarize natural CO2 fixation pathways, provide a roadmap for the design and implementation of artificial carbon fixation pathways, and highlight examples of biocatalytic cascades involving carboxylases. Additionally, we suggest that biochemical utilization of reduced CO2 derivates, such as formate or methanol, represents a suitable alternative to direct use of CO2 and provide several examples. Our discussion closes with a techno-economic perspective on enzymatic CO2 fixation and its potential to reduce CO2 emissions.
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Affiliation(s)
- Sarah Bierbaumer
- Institute of Chemistry, University of Graz, NAWI Graz, Heinrichstraße 28, 8010 Graz, Austria
| | - Maren Nattermann
- Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Straße 10, 35043 Marburg, Germany
| | - Luca Schulz
- Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Straße 10, 35043 Marburg, Germany
| | | | - Tobias J Erb
- Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Straße 10, 35043 Marburg, Germany
| | - Christoph K Winkler
- Institute of Chemistry, University of Graz, NAWI Graz, Heinrichstraße 28, 8010 Graz, Austria
| | - Matthias Tinzl
- Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Straße 10, 35043 Marburg, Germany
| | - Silvia M Glueck
- Institute of Chemistry, University of Graz, NAWI Graz, Heinrichstraße 28, 8010 Graz, Austria
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22
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Arnold PK, Finley LW. Regulation and function of the mammalian tricarboxylic acid cycle. J Biol Chem 2022; 299:102838. [PMID: 36581208 PMCID: PMC9871338 DOI: 10.1016/j.jbc.2022.102838] [Citation(s) in RCA: 53] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 12/15/2022] [Accepted: 12/20/2022] [Indexed: 12/27/2022] Open
Abstract
The tricarboxylic acid (TCA) cycle, otherwise known as the Krebs cycle, is a central metabolic pathway that performs the essential function of oxidizing nutrients to support cellular bioenergetics. More recently, it has become evident that TCA cycle behavior is dynamic, and products of the TCA cycle can be co-opted in cancer and other pathologic states. In this review, we revisit the TCA cycle, including its potential origins and the history of its discovery. We provide a detailed accounting of the requirements for sustained TCA cycle function and the critical regulatory nodes that can stimulate or constrain TCA cycle activity. We also discuss recent advances in our understanding of the flexibility of TCA cycle wiring and the increasingly appreciated heterogeneity in TCA cycle activity exhibited by mammalian cells. Deeper insight into how the TCA cycle can be differentially regulated and, consequently, configured in different contexts will shed light on how this pathway is primed to meet the requirements of distinct mammalian cell states.
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Affiliation(s)
- Paige K. Arnold
- Cell Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York, USA,Louis V. Gerstner Jr. Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Lydia W.S. Finley
- Cell Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York, USA,For correspondence: Lydia W. S. Finley
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23
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Pettinato E, Böhnert P, Berg IA. Succinyl-CoA:acetate CoA-transferase functioning in the oxidative tricarboxylic acid cycle in Desulfurella acetivorans. Front Microbiol 2022; 13:1080142. [PMID: 36569052 PMCID: PMC9768450 DOI: 10.3389/fmicb.2022.1080142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 11/22/2022] [Indexed: 12/12/2022] Open
Abstract
Desulfurella acetivorans is a strictly anaerobic sulfur-reducing deltaproteobacterium that possesses a very dynamic metabolism with the ability to revert the citrate synthase version of the tricarboxylic acid (TCA) cycle for autotrophic growth (reversed oxidative TCA cycle) or to use it for acetate oxidation (oxidative TCA cycle). Here we show that for heterotrophic growth on acetate D. acetivorans uses a modified oxidative TCA cycle that was first discovered in acetate-oxidizing sulfate reducers in which a succinyl-CoA:acetate CoA-transferase catalyzes the conversion of succinyl-CoA to succinate, coupled with the activation of acetate to acetyl-CoA. We identified the corresponding enzyme in this bacterium as the AHF96498 gene product and characterized it biochemically. Our phylogenetic analysis of CoA-transferases revealed that the CoA-transferase variant of the oxidative TCA cycle has convergently evolved several times in different bacteria. Its functioning is especially important for anaerobes, as it helps to increase the energetic efficiency of the pathway by using one enzyme for two enzymatic reactions and by allowing to spend just one ATP equivalent for acetate activation.
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24
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Bsharat O, Doyle MGJ, Munch M, Mair BA, Cooze CJC, Derdau V, Bauer A, Kong D, Rotstein BH, Lundgren RJ. Aldehyde-catalysed carboxylate exchange in α-amino acids with isotopically labelled CO 2. Nat Chem 2022; 14:1367-1374. [PMID: 36344821 DOI: 10.1038/s41557-022-01074-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 09/23/2022] [Indexed: 11/09/2022]
Abstract
The isotopic labelling of small molecules is integral to drug development and for understanding biochemical processes. The preparation of carbon-labelled α-amino acids remains difficult and time consuming, with established methods involving label incorporation at an early stage of synthesis. This explains the high cost and scarcity of C-labelled products and presents a major challenge in 11C applications (11C t1/2 = 20 min). Here we report that aldehydes catalyse the isotopic carboxylate exchange of native α-amino acids with *CO2 (* = 14, 13, 11). Proteinogenic α-amino acids and many non-natural variants containing diverse functional groups undergo labelling. The reaction probably proceeds via the trapping of *CO2 by imine-carboxylate intermediates to generate iminomalonates that are prone to monodecarboxylation. Tempering catalyst electrophilicity was key to preventing irreversible aldehyde consumption. The pre-generation of the imine carboxylate intermediate allows for the rapid and late-stage 11C-radiolabelling of α-amino acids in the presence of [11C]CO2.
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Affiliation(s)
- Odey Bsharat
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada
| | - Michael G J Doyle
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada
| | - Maxime Munch
- Department of Biochemistry, Microbiology and Immunology and Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, Ontario, Canada
- University of Ottawa Heart Institute, Ottawa, Ontario, Canada
| | - Braeden A Mair
- Department of Biochemistry, Microbiology and Immunology and Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, Ontario, Canada
- University of Ottawa Heart Institute, Ottawa, Ontario, Canada
| | | | - Volker Derdau
- Sanofi-Aventis Deutschland GmbH, R&D, Integrated Drug Discovery, Isotope Chemistry, Industriepark Höchst, Frankfurt, Germany
| | - Armin Bauer
- Sanofi-Aventis Deutschland GmbH, R&D, Integrated Drug Discovery, Isotope Chemistry, Industriepark Höchst, Frankfurt, Germany
| | - Duanyang Kong
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada
| | - Benjamin H Rotstein
- Department of Biochemistry, Microbiology and Immunology and Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, Ontario, Canada.
- University of Ottawa Heart Institute, Ottawa, Ontario, Canada.
| | - Rylan J Lundgren
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada.
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25
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McCall CE, Zhu X, Zabalawi M, Long D, Quinn MA, Yoza BK, Stacpoole PW, Vachharajani V. Sepsis, pyruvate, and mitochondria energy supply chain shortage. J Leukoc Biol 2022; 112:1509-1514. [PMID: 35866365 PMCID: PMC9796618 DOI: 10.1002/jlb.3mr0322-692rr] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 06/24/2022] [Accepted: 06/28/2022] [Indexed: 01/04/2023] Open
Abstract
Balancing high energy-consuming danger resistance and low energy supply of disease tolerance is a universal survival principle that often fails during sepsis. Our research supports the concept that sepsis phosphorylates and deactivates mitochondrial pyruvate dehydrogenase complex control over the tricarboxylic cycle and the electron transport chain. StimulatIng mitochondrial energetics in septic mice and human sepsis cell models can be achieved by inhibiting pyruvate dehydrogenase kinases with the pyruvate structural analog dichloroacetate. Stimulating the pyruvate dehydrogenase complex by dichloroacetate reverses a disruption in the tricarboxylic cycle that induces itaconate, a key mediator of the disease tolerance pathway. Dichloroacetate treatment increases mitochondrial respiration and ATP synthesis, decreases oxidant stress, overcomes metabolic paralysis, regenerates tissue, organ, and innate and adaptive immune cells, and doubles the survival rate in a murine model of sepsis.
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Affiliation(s)
- Charles E. McCall
- Department of MedicineWake Forest School of MedicineWinston SalemNCUSA
| | - Xuewei Zhu
- Department of MedicineWake Forest School of MedicineWinston SalemNCUSA
| | - Manal Zabalawi
- Department of MedicineWake Forest School of MedicineWinston SalemNCUSA
| | - David Long
- Department of MedicineWake Forest School of MedicineWinston SalemNCUSA
| | - Matthew A. Quinn
- Department of Pathology – Comparative MedicineWake Forest School of MedicineWinston SalemNCUSA
| | - Barbara K. Yoza
- Department of SurgeryWake Forest School of MedicineWinston SalemNCUSA
| | - Peter W. Stacpoole
- Department of Medicine and BiochemistryUniversity of Florida Medical SchoolGainesvilleFloridaUSA
| | - Vidula Vachharajani
- Department of Critical Care MedicineCleveland Clinic Lerner College of Medicine of CWRUClevelandOhioUSA
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26
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Narrowing gaps between Earth and life. Proc Natl Acad Sci U S A 2022; 119:e2216017119. [PMID: 36288265 PMCID: PMC9674954 DOI: 10.1073/pnas.2216017119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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27
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Screening for Hyperthermophilic Electrotrophs for the Microbial Electrosynthesis of Organic Compounds. Microorganisms 2022; 10:microorganisms10112249. [DOI: 10.3390/microorganisms10112249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 11/07/2022] [Accepted: 11/10/2022] [Indexed: 11/16/2022] Open
Abstract
Microbial electrosynthesis has recently emerged as a promising technology for the sustainable production of organic acids, bioplastics, or biofuels from electricity and CO2. However, the diversity of catalysts and metabolic pathways is limited to mainly mesophilic acetogens or methanogens. Here, eleven hyperthermophilic strains related to Archaeoglobales, Thermococcales, Aquificales, and methanogens were screened for microbial electrosynthesis. The strains were previously isolated from deep-sea hydrothermal vents, where a naturally occurring, spontaneous electrical current can serve as a source of energy for microbial metabolism. After 6 days of incubation in an electrochemical system, all strains showed current consumption, biofilm formation, and small organic molecule production relative to the control. Six selected strains were then incubated over a longer period of time. In the course of one month, a variety of metabolic intermediates of biotechnological relevance such as succinic acid and glycerol accumulated. The production rates and the promotion of specific metabolic pathways seemed to be influenced by the experimental conditions, such as the concentration of CO2 in the gas phase and electron acceptor limitation. Further work is necessary to clearly identify these effects to potentially be able to tune the microbial electrosynthesis of compounds of interest.
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28
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Cai S, Liu M, Zhang Y, Hu A, Zhang W, Wang D. Molecular transformation of dissolved organic matter and formation pathway of humic substances in dredged sludge under aerobic composting. BIORESOURCE TECHNOLOGY 2022; 364:128141. [PMID: 36257519 DOI: 10.1016/j.biortech.2022.128141] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Revised: 10/08/2022] [Accepted: 10/11/2022] [Indexed: 06/16/2023]
Abstract
Using Fourier transform-ion cyclotron resonance mass spectrometry (FT-ICR MS) and molecular reaction network analysis, this study investigated molecular transformation of dissolved organic matter (DOM) and formation pathway of humic substances (HS) in dredged sludge during aerobic composting. The results showed that macromolecular N-containing compounds in dredged sludge are abundantly transformed into unsaturated and aromatic oxygenated compounds, exhibiting physicochemical properties similar to those of humus. Especially, N-containing compounds with one nitrogen atom are susceptible to oxidative deamination. Furthermore, assemblages of reactive fragments (e.g., -C7H8O2, -C10H12O2, -C2H2O2, and -C4H6O2) were identified as potential precursors to HS formed by the following reactions: starting with protein deamination and desulfurization, lignin delignification cascaded, finally decarbonylation occurred. This work provides novel insight for optimizing the process of stabilization and humification of dredged sludge.
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Affiliation(s)
- Siying Cai
- School of Environmental Studies, China University of Geosciences, Wuhan 430074, Hubei, China
| | - Ming Liu
- School of Environmental Studies, China University of Geosciences, Wuhan 430074, Hubei, China; Beijing Machinery & Electricity Institute Co., Ltd, Beijing 100020, China
| | - Yu Zhang
- School of Environmental Studies, China University of Geosciences, Wuhan 430074, Hubei, China
| | - Aibin Hu
- School of Environmental Studies, China University of Geosciences, Wuhan 430074, Hubei, China
| | - Weijun Zhang
- School of Environmental Studies, China University of Geosciences, Wuhan 430074, Hubei, China; Hubei Key Laboratory of Yangtze Catchment Environmental Aquatic Science, School of Environmental Studies, China University of Geosciences, Wuhan 430074, Hubei, China; State Environmental Protection Key Laboratory of Source Apportionment and Control of Aquatic Pollution, Ministry of Ecology and Environment, Wuhan 430074, Hubei, China.
| | - Dongsheng Wang
- Department of Environmental Engineering, Zhejiang University, Hangzhou 310058, Zhejiang, China
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29
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Chen X, Tang K, Zhang M, Liu S, Chen M, Zhan P, Fan W, Chen CTA, Zhang Y. Genome-centric insight into metabolically active microbial population in shallow-sea hydrothermal vents. MICROBIOME 2022; 10:170. [PMID: 36242065 PMCID: PMC9563475 DOI: 10.1186/s40168-022-01351-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 08/22/2022] [Indexed: 05/20/2023]
Abstract
BACKGROUND Geothermal systems have contributed greatly to both our understanding of the functions of extreme life and the evolutionary history of life itself. Shallow-sea hydrothermal systems are ecological intermediates of deep-sea systems and terrestrial springs, harboring unique and complexed ecosystems, which are well-lit and present physicochemical gradients. The microbial communities of deep-sea and terrestrial geothermal systems have been well-studied at the population genome level, yet little is known about the communities inhabiting the shallow-sea hydrothermal systems and how they compare to those inhabiting other geothermal systems. RESULTS Here, we used genome-resolved metagenomic and metaproteomic approaches to probe into the genetic potential and protein expression of microorganisms from the shallow-sea vent fluids off Kueishantao Island. The families Nautiliaceae and Campylobacteraceae within the Epsilonbacteraeota and the Thiomicrospiraceae within the Gammaproteobacteria were prevalent in vent fluids over a 3-year sampling period. We successfully reconstructed the in situ metabolic modules of the predominant populations within the Epsilonbacteraeota and Gammaproteobacteria by mapping the metaproteomic data back to metagenome-assembled genomes. Those active bacteria could use the reductive tricarboxylic acid cycle or Calvin-Benson-Bassham cycle for autotrophic carbon fixation, with the ability to use reduced sulfur species, hydrogen or formate as electron donors, and oxygen as a terminal electron acceptor via cytochrome bd oxidase or cytochrome bb3 oxidase. Comparative metagenomic and genomic analyses revealed dramatic differences between submarine and terrestrial geothermal systems, including microbial functional potentials for carbon fixation and energy conversion. Furthermore, shallow-sea hydrothermal systems shared many of the major microbial genera that were first isolated from deep-sea and terrestrial geothermal systems, while deep-sea and terrestrial geothermal systems shared few genera. CONCLUSIONS The metabolic machinery of the active populations within Epsilonbacteraeota and Gammaproteobacteria at shallow-sea vents can mirror those living at deep-sea vents. With respect to specific taxa and metabolic potentials, the microbial realm in the shallow-sea hydrothermal system presented ecological linkage to both deep-sea and terrestrial geothermal systems. Video Abstract.
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Affiliation(s)
- Xiaofeng Chen
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Science, Xiamen University, Xiamen, China
| | - Kai Tang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Science, Xiamen University, Xiamen, China.
| | - Mu Zhang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Science, Xiamen University, Xiamen, China
| | - Shujing Liu
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Science, Xiamen University, Xiamen, China
| | - Mingming Chen
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Science, Xiamen University, Xiamen, China
| | - Peiwen Zhan
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Science, Xiamen University, Xiamen, China
| | - Wei Fan
- Ocean College, Zhejiang University, Zhoushan, China
| | - Chen-Tung Arthur Chen
- Institute of Marine Geology and Chemistry, National Sun Yat-Sen University, Taiwan, China
| | - Yao Zhang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Science, Xiamen University, Xiamen, China
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30
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Yang Z, Leero DD, Yin C, Yang L, Zhu L, Zhu Z, Jiang L. Clostridium as microbial cell factory to enable the sustainable utilization of three generations of feedstocks. BIORESOURCE TECHNOLOGY 2022; 361:127656. [PMID: 35872277 DOI: 10.1016/j.biortech.2022.127656] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 07/15/2022] [Accepted: 07/16/2022] [Indexed: 06/15/2023]
Abstract
The sustainable production of chemicals and biofuels from non-fossil carbon sources is considered key to reducing greenhouse gas (GHG) emissions. Clostridium sp. can convert various substrates, including the 1st-generation (biomass crops), the 2nd-generation (lignocellulosic biomass), and the 3rd-generation (C1 gases) feedstocks, into high-value products, which makes Clostridia attractive for biorefinery applications. However, the complexity of lignocellulosic catabolism and C1 gas utilization make it difficult to construct efficient production routes. Accordingly, this review highlights the advances in the development of three generations of feedstocks with Clostridia as cell factories. At the same time, more attention was given to using agro-industrial wastes (lignocelluloses and C1 gases) as the feedstocks, for which metabolic and process engineering efforts were comprehensively analyzed. In addition, the challenges of using agro-industrial wastes are also discussed. Lastly, several new synthetic biology tools and regulatory strategies are emphasized as promising technologies to be developed to address the aforementioned challenges in Clostridia and realize the efficient utilization of agro-industrial wastes.
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Affiliation(s)
- Zhihan Yang
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, China
| | - Donald Delano Leero
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, China
| | - Chengtai Yin
- College of Overseas Education, Nanjing Tech University, Nanjing 211816, China
| | - Lei Yang
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, China
| | - Liying Zhu
- College of Chemical and Molecular Engineering, Nanjing Tech University, Nanjing 211816, China
| | - Zhengming Zhu
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, China
| | - Ling Jiang
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, China; State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing 211816, China.
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31
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Ragab EM, El Gamal DM, Mohamed TM, Khamis AA. Therapeutic potential of chrysin nanoparticle-mediation inhibition of succinate dehydrogenase and ubiquinone oxidoreductase in pancreatic and lung adenocarcinoma. Eur J Med Res 2022; 27:172. [PMID: 36076266 PMCID: PMC9461199 DOI: 10.1186/s40001-022-00803-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Accepted: 08/30/2022] [Indexed: 12/04/2022] Open
Abstract
Pancreatic adenocarcinoma (PDAC) and lung cancer are expected to represent the most common cancer types worldwide until 2030. Under typical conditions, mitochondria provide the bulk of the energy needed to sustain cell life. For that inhibition of mitochondrial complex ΙΙ (CΙΙ) and ubiquinone oxidoreductase with natural treatments may represent a promising cancer treatment option. A naturally occurring flavonoid with biological anti-cancer effects is chyrsin. Due to their improved bioavailability, penetrative power, and efficacy, chitosan–chrysin nano-formulations (CCNPs) are being used in medicine with increasing frequency. Chitosan (cs) is also regarded as a highly versatile and adaptable polymer. The cationic properties of Cs, together with its biodegradability, high adsorption capacity, biocompatibility, effect on permeability, ability to form films, and adhesive properties, are advantages. In addition, Cs is thought to be both safe and economical. CCNPs may indeed be therapeutic candidates in the treatment of pancreatic adenocarcinoma (PDAC) and lung cancer by blocking succinate ubiquinone oxidoreductase.
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Affiliation(s)
- Eman M Ragab
- Biochemistry Division, Chemistry Department, Faculty of Science, Tanta University, Tanta, 31527, Egypt.
| | - Doaa M El Gamal
- Biochemistry Division, Chemistry Department, Faculty of Science, Tanta University, Tanta, 31527, Egypt
| | - Tarek M Mohamed
- Biochemistry Division, Chemistry Department, Faculty of Science, Tanta University, Tanta, 31527, Egypt
| | - Abeer A Khamis
- Biochemistry Division, Chemistry Department, Faculty of Science, Tanta University, Tanta, 31527, Egypt.
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32
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He Y, Zhang Y, Li T, Peng X, Jia X. High-concentration COD wastewater treatment with simultaneous removal of nitrogen and phosphorus by a novel Candida tropicalis strain: Removal capability and mechanism. ENVIRONMENTAL RESEARCH 2022; 212:113471. [PMID: 35613633 DOI: 10.1016/j.envres.2022.113471] [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: 12/27/2021] [Revised: 04/25/2022] [Accepted: 05/10/2022] [Indexed: 06/15/2023]
Abstract
Aerobic and anaerobic continuous stirred-tank reactor (CSTR), up-flow anaerobic sludge blanket (UASB) were set up and inoculated with newly isolated Candida tropicalis. Reactors were operated at high concentrations of chemical oxygen demand (COD) (8000 mg/L), the modified UASB expressed better COD removal rate simultaneously removal of nitrogen and phosphate than other two reactors. Notably, under both aerobic or anaerobic conditions, large amounts of organic acids and alcohol were generated. Transcriptomic analysis showed that carbon metabolism under anaerobic conditions shared the same pathway with aerobic conditions by regulating and inhibiting some functional genes. Experiments utilizing different carbon sources proved that our strain has excellent performances in utilizing organic materials, which were verified by transcriptomic analysis. Finally, the strain was applied to treat four types of sugar-containing wastewaters. Among them, our strain exerts the best removal capability of COD (90%), nitrogen (89%), and phosphate (82%) for brewery wastewater.
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Affiliation(s)
- Yuzhe He
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, 510006, China
| | - Yaqi Zhang
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, 510006, China
| | - Tianyu Li
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, 510006, China
| | - Xingxing Peng
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, 510006, China; Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou, 510275, China.
| | - Xiaoshan Jia
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, 510006, China; Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou, 510275, China.
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33
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Rosado-Porto D, Ratering S, Moser G, Deppe M, Müller C, Schnell S. Soil metatranscriptome demonstrates a shift in C, N, and S metabolisms of a grassland ecosystem in response to elevated atmospheric CO2. Front Microbiol 2022; 13:937021. [PMID: 36081791 PMCID: PMC9445814 DOI: 10.3389/fmicb.2022.937021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 08/01/2022] [Indexed: 11/16/2022] Open
Abstract
Soil organisms play an important role in the equilibrium and cycling of nutrients. Because elevated CO2 (eCO2) affects plant metabolism, including rhizodeposition, it directly impacts the soil microbiome and microbial processes. Therefore, eCO2 directly influences the cycling of different elements in terrestrial ecosystems. Hence, possible changes in the cycles of carbon (C), nitrogen (N), and sulfur (S) were analyzed, alongside the assessment of changes in the composition and structure of the soil microbiome through a functional metatranscriptomics approach (cDNA from mRNA) from soil samples taken at the Giessen free-air CO2 enrichment (Gi-FACE) experiment. Results showed changes in the expression of C cycle genes under eCO2 with an increase in the transcript abundance for carbohydrate and amino acid uptake, and degradation, alongside an increase in the transcript abundance for cellulose, chitin, and lignin degradation and prokaryotic carbon fixation. In addition, N cycle changes included a decrease in the transcript abundance of N2O reductase, involved in the last step of the denitrification process, which explains the increase of N2O emissions in the Gi-FACE. Also, a shift in nitrate (NO3-) metabolism occurred, with an increase in transcript abundance for the dissimilatory NO3- reduction to ammonium (NH4+) (DNRA) pathway. S metabolism showed increased transcripts for sulfate (SO42-) assimilation under eCO2 conditions. Furthermore, soil bacteriome, mycobiome, and virome significantly differed between ambient and elevated CO2 conditions. The results exhibited the effects of eCO2 on the transcript abundance of C, N, and S cycles, and the soil microbiome. This finding showed a direct connection between eCO2 and the increased greenhouse gas emission, as well as the importance of soil nutrient availability to maintain the balance of soil ecosystems.
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Affiliation(s)
- David Rosado-Porto
- Institute of Applied Microbiology, Justus Liebig University, Giessen, Germany
- Faculty of Basic and Biomedical Sciences, Simón Bolívar University, Barranquilla, Colombia
| | - Stefan Ratering
- Institute of Applied Microbiology, Justus Liebig University, Giessen, Germany
| | - Gerald Moser
- Institute of Plant Ecology, Justus Liebig University, Giessen, Germany
| | - Marianna Deppe
- Institute of Plant Ecology, Justus Liebig University, Giessen, Germany
| | - Christoph Müller
- Institute of Plant Ecology, Justus Liebig University, Giessen, Germany
- School of Biology and Environmental Science and Earth Institute, University College Dublin, Dublin, Ireland
| | - Sylvia Schnell
- Institute of Applied Microbiology, Justus Liebig University, Giessen, Germany
- *Correspondence: Sylvia Schnell
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Zhou L, Lai Y, Zeng R, Zhao B, Jian Y, Ou P, Zhang W, Ng HY, Zhuang WQ. Core carbon fixation pathways associated with cake layer development in an anoxic-oxic biofilm-membrane bioreactor treating textile wastewater. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 835:155483. [PMID: 35483462 DOI: 10.1016/j.scitotenv.2022.155483] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 04/17/2022] [Accepted: 04/19/2022] [Indexed: 06/14/2023]
Abstract
Microbial carbon fixation pathways have not yet been adequately understood for their role in membrane case layer formation processes. Carbon fixation bacteria can play critical roles in either causing or enhancing cake layer formation in some autotrophic-prone anoxic conditions, such as sulfur-cycling conditions. Understanding the microbes capable of carbon fixation can potentially guide the design of membrane biofouling mitigation strategies in scientific ways. Thus, we used meta-omics methods to query carbon fixation pathways in the cake layers of a full-scale anoxic-oxic biofilm-MBR system treating textile wastewater in this study. Based on the wastewater constituents and other properties, such as anoxic conditions, sulfide-reducing and sulfur-oxidizing bacteria could co-exist in the membrane unit. In addition, low-light radiation conditions could also happen to the membrane unit. However, we could not quantify the light intensity or total energy input accurately because the whole experimental setup was a full-scale system. Potentially complete carbon fixation pathways in the cake layer included the Calvin-Benson-Bassham cycle, Wood-Ljungdahl pathway, and the 3-hydroxypropionate bicycle. We discovered that using aeration could effectively inhibit carbon fixation, which resulted in mitigating membrane cake layer development. However, the aeration resulted in the 3-hydroxypropionate bicycle pathway, presumably used by aerobic sulfur-oxidizing prokaryotes, to become a more abundant carbon fixation pathway in the cake layer under aerobic conditions.
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Affiliation(s)
- Lijie Zhou
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen 518060, China.
| | - Yongzhou Lai
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen 518060, China
| | - Rongjie Zeng
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen 518060, China
| | - Bikai Zhao
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen 518060, China
| | - Yixin Jian
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen 518060, China
| | - Pingxiang Ou
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen 518060, China
| | - Wenyu Zhang
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen 518060, China
| | - How Yong Ng
- Centre for Water Research, Department of Civil & Environmental Engineering, National University of Singapore, 1 Engineering Drive 2, 117576, Singapore.
| | - Wei-Qin Zhuang
- Department of Civil and Environmental Engineering, The University of Auckland, Auckland 1142, New Zealand
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35
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An international comprehensive benchmarking analysis of synthetic biology in China from 2015 to 2020. Chin J Chem Eng 2022. [DOI: 10.1016/j.cjche.2021.05.036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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36
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Tang L, Su C, Fan C, Li R, Wang Y, Gao S, Chen M. Long-term effect of perfluorooctanoic acid on the anammox system based on metagenomics: Performance, sludge characteristic and microbial community dynamic. BIORESOURCE TECHNOLOGY 2022; 351:127002. [PMID: 35292384 DOI: 10.1016/j.biortech.2022.127002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 03/10/2022] [Accepted: 03/10/2022] [Indexed: 06/14/2023]
Abstract
The effects of PFOA on the nitrogen removal performance, microbial community and functional genes of anaerobic ammonium oxidation (anammox) sludge in an anaerobic baffled reactor (ABR) were investigated. The removal efficiencies of ammonia nitrogen (NH4+-N) and nitrite (NO2--N) decreased from 93.90 ± 3.64% and 98.6 ± 1.84% to 77.81 ± 6.86% and 77.96 ± 1.88% when PFOA increased from 5 mg/L to 50 mg/L, respectively. X-ray photoelectron spectra analysis of the anammox sludge showed the presence of both C-F and CaF2 forms of F. Metagenomics analysis of the anammox sludge in the first compartment illustrated that the relative abundance of Ca.Brocadia and Ca.Kuenenia decreased from 22.21% and 5.61% to 2.11% and 2.84% at 50 mg/L PFOA compared with that without PFOA. In addition, the nitrogen metabolism pathway showed that adding 50 mg/L PFOA decreased the expression of HzsB, HzsC, and Hdh (anammox genes) by 0.096%, 0.05% and 0.062%, respectively.
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Affiliation(s)
- Linqin Tang
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, 15 Yucai Road, Guilin 541004, PR China
| | - Chengyuan Su
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, 15 Yucai Road, Guilin 541004, PR China; University Key Laboratory of Karst Ecology and Environmental Change of Guangxi Province (Guangxi Normal University), 15 Yucai Road, Guilin 541004, PR China.
| | - Cuiping Fan
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, 15 Yucai Road, Guilin 541004, PR China
| | - Ruting Li
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, 15 Yucai Road, Guilin 541004, PR China
| | - Yuchen Wang
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, 15 Yucai Road, Guilin 541004, PR China
| | - Shu Gao
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, 15 Yucai Road, Guilin 541004, PR China
| | - Menglin Chen
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, 15 Yucai Road, Guilin 541004, PR China
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Spring S, Rohde M, Bunk B, Spröer C, Will SE, Neumann-Schaal M. New insights into the energy metabolism and taxonomy of Deferribacteres revealed by the characterization of a new isolate from a hypersaline microbial mat. Environ Microbiol 2022; 24:2543-2575. [PMID: 35415868 DOI: 10.1111/1462-2920.15999] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 04/04/2022] [Indexed: 12/13/2022]
Abstract
Strain L21-Ace-BEST , isolated from a lithifying cyanobacterial mat, could be assigned to a novel species and genus within the Deferribacteres. It is an important model organism for the study of anaerobic acetate degradation under hypersaline conditions. The metabolism of strain L21-Ace-BEST was characterized by biochemical studies, comparative genome analyses, and the evaluation of gene expression patterns. The central metabolic pathway is the citric acid cycle, which is mainly controlled by the enzyme succinyl-CoA:acetate-CoA transferase. The potential use of a reversed oxidative citric acid cycle to fix CO2 has been revealed through genome analysis. However, no autotrophic growth was detected in this strain, whereas sulfide and H2 can be used mixotrophically. Preferred electron acceptors for the anaerobic oxidation of acetate are nitrate, fumarate and DMSO, while oxygen can be utilized only under microoxic conditions. Aerotolerant growth by fermentation was observed at higher oxygen concentrations. The redox cycling of sulfur/sulfide enables the generation of reducing power for the assimilation of acetate during growth and could prevent the over-reduction of cells in stationary phase. Extracellular electron transfer appears to be an essential component of the respiratory metabolism in this clade of Deferribacteres and may be involved in the reduction of nitrite to ammonium. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Stefan Spring
- Department Microorganisms, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Manfred Rohde
- Central Facility for Microscopy, Helmholtz Centre for Infection Research, HZI, Braunschweig, Germany
| | - Boyke Bunk
- Department Bioinformatics, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Cathrin Spröer
- Department Bioinformatics, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Sabine Eva Will
- Research Group Metabolomics, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Meina Neumann-Schaal
- Research Group Metabolomics, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
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Steffens L, Pettinato E, Steiner TM, Eisenreich W, Berg IA. Tracking the Reversed Oxidative Tricarboxylic Acid Cycle in Bacteria. Bio Protoc 2022; 12:e4364. [PMID: 35434198 PMCID: PMC8983159 DOI: 10.21769/bioprotoc.4364] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Revised: 11/22/2021] [Accepted: 02/10/2022] [Indexed: 12/29/2022] Open
Abstract
Different pathways for autotrophic CO2 fixation can be recognized by the presence of genes for their specific key enzymes. On this basis, (meta)genomic, (meta)transcriptomic, or (meta)proteomic analysis enables the identification of the role of an organism or a distinct pathway in primary production. However, the recently discovered variant of the reductive tricarboxylic acid (rTCA) cycle, the reverse oxidative tricarboxylic acid (roTCA) cycle, lacks unique enzymes, a feature that makes it cryptic for bioinformatics analysis. This pathway is a reversal of the widespread tricarboxylic acid (TCA) cycle. The functioning of the roTCA cycle requires unusually high activity of citrate synthase, the enzyme responsible for citrate cleavage, as well as elevated CO2 partial pressures. Here, we present a detailed description of the protocol we used for the identification of the roTCA cycle in members of Desulfurellaceae. First, we describe the anaerobic cultivation of Desulfurellaceae at different CO2 concentrations with a method that can be adapted to the cultivation of other anaerobes. Then, we explain how to measure activities of enzymes responsible for citrate cleavage, malate dehydrogenase reaction, and the crucial carboxylation step of the cycle catalyzed by pyruvate synthase in cell extracts. In conclusion, we describe stable isotope experiments that allow tracking of the roTCA cycle in vivo, through the position-specific incorporation of carbon-13 into amino acids. The label is provided to the organism as 13CO2 or [1-13C]glutamate. The same key methodology can be used for the reliable evaluation of the functioning of the roTCA cycle in any organism under study. This pathway is likely to participate, completely unseen, in the metabolism of various microorganisms. Graphic abstract.
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Affiliation(s)
- Lydia Steffens
- Institute for Molecular Microbiology and Biotechnology, University of Münster, Münster, Germany
| | - Eugenio Pettinato
- Institute for Molecular Microbiology and Biotechnology, University of Münster, Münster, Germany
| | - Thomas M. Steiner
- Bavarian NMR Center–Structural Membrane Biochemistry, Department of Chemistry, Technische Universität München, Garching, Germany
| | - Wolfgang Eisenreich
- Bavarian NMR Center–Structural Membrane Biochemistry, Department of Chemistry, Technische Universität München, Garching, Germany
,
*For correspondence: ;
| | - Ivan A. Berg
- Institute for Molecular Microbiology and Biotechnology, University of Münster, Münster, Germany
,
*For correspondence: ;
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39
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Cyanide as a primordial reductant enables a protometabolic reductive glyoxylate pathway. Nat Chem 2022; 14:170-178. [PMID: 35115655 DOI: 10.1038/s41557-021-00878-w] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 12/14/2021] [Indexed: 11/08/2022]
Abstract
Investigation of prebiotic metabolic pathways is predominantly based on abiotically replicating the reductive citric acid cycle. While attractive from a parsimony point of view, attempts using metal/mineral-mediated reductions have produced complex mixtures with inefficient and uncontrolled reactions. Here we show that cyanide acts as a mild and efficient reducing agent mediating abiotic transformations of tricarboxylic acid intermediates and derivatives. The hydrolysis of the cyanide adducts followed by their decarboxylation enables the reduction of oxaloacetate to malate and of fumarate to succinate, whereas pyruvate and α-ketoglutarate themselves are not reduced. In the presence of glyoxylate, malonate and malononitrile, alternative pathways emerge that bypass the challenging reductive carboxylation steps to produce metabolic intermediates and compounds found in meteorites. These results suggest a simpler prebiotic forerunner of today's metabolism, involving a reductive glyoxylate pathway without oxaloacetate and α-ketoglutarate-implying that the extant metabolic reductive carboxylation chemistries are an evolutionary invention mediated by complex metalloproteins.
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40
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Microorganisms harbor keys to a circular bioeconomy making them useful tools in fighting plastic pollution and rising CO 2 levels. Extremophiles 2022; 26:10. [PMID: 35118556 PMCID: PMC8813813 DOI: 10.1007/s00792-022-01261-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 01/21/2022] [Indexed: 12/19/2022]
Abstract
The major global and man-made challenges of our time are the fossil fuel-driven climate change a global plastic pollution and rapidly emerging plant, human and animal infections. To meet the necessary global changes, a dramatic transformation must take place in science and society. This transformation will involve very intense and forward oriented industrial and basic research strongly focusing on (bio)technology and industrial bioprocesses developments towards engineering a zero-carbon sustainable bioeconomy. Within this transition microorganisms-and especially extremophiles-will play a significant and global role as technology drivers. They harbor the keys and blueprints to a sustainable biotechnology in their genomes. Within this article, we outline urgent and important areas of microbial research and technology advancements and that will ultimately make major contributions during the transition from a linear towards a circular bioeconomy.
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41
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Zhu J, Yan X, Zhou L, Li N, Liao C, Wang X. Insight of bacteria and archaea in Feammox community enriched from different soils. ENVIRONMENTAL RESEARCH 2022; 203:111802. [PMID: 34343555 DOI: 10.1016/j.envres.2021.111802] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 07/26/2021] [Accepted: 07/27/2021] [Indexed: 06/13/2023]
Abstract
Anaerobic ammonium oxidation coupled to Fe(III) reduction, known as Feammox, is a newly discovered nitrogen-cycling process, which serves an important role in the pathways of nitrogen loss in the environment. However, the specific types of microorganisms involved in Feammox currently remain unclear. In this study, we selected two groups of soil samples (paddy and mine), from considerably different habitats in South China, to acclimate Feammox colonies. The Paddy Group had a shorter lag period than the Mine Group, while the ammonium transformation rate was nearly equal in both groups in the mature period. The emergence of the Feammox activity was found to be associated with the increased abundance of iron-reducing bacteria, especially Clostridium_sensu_stricto_12, Desulfitobacterium, Thermoanaerobaculum, Anaeromyxobacter and Geobacter. Ammonium oxidizing archaea and methanogens were dominant among the known archaea. These findings extend our knowledge of the microbial community composition of the potential Feammox microbes from soils under different environmental conditions, which broadens our understanding of this important Fe/N transformation process.
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Affiliation(s)
- Jiaxuan Zhu
- MOE Key Laboratory of Pollution Processes and Environmental Criteria/Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, No. 38 Tongyan Road, Jinnan District, Tianjin, 300350, China
| | - Xuejun Yan
- MOE Key Laboratory of Pollution Processes and Environmental Criteria/Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, No. 38 Tongyan Road, Jinnan District, Tianjin, 300350, China
| | - Lean Zhou
- School of Hydraulic Engineering, Changsha University of Science & Technology, Changsha, 410114, China
| | - Nan Li
- School of Environmental Science and Engineering, Tianjin University, No. 92 Weijin Road, Nankai District, Tianjin, 300072, China
| | - Chengmei Liao
- MOE Key Laboratory of Pollution Processes and Environmental Criteria/Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, No. 38 Tongyan Road, Jinnan District, Tianjin, 300350, China.
| | - Xin Wang
- MOE Key Laboratory of Pollution Processes and Environmental Criteria/Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, No. 38 Tongyan Road, Jinnan District, Tianjin, 300350, China.
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42
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Xu Y, Ren J, Wang W, Zeng A. Improvement of glycine biosynthesis from one-carbon compounds and ammonia catalyzed by the glycine cleavage system in vitro. Eng Life Sci 2022; 22:40-53. [PMID: 35024026 PMCID: PMC8727733 DOI: 10.1002/elsc.202100047] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Revised: 08/25/2021] [Accepted: 10/28/2021] [Indexed: 12/26/2022] Open
Abstract
Glycine cleavage system (GCS) plays a central role in one-carbon (C1) metabolism and receives increasing interest as a core part of the recently proposed reductive glycine pathway (rGlyP) for assimilation of CO2 and formate. Despite decades of research, GCS has not yet been well understood and kinetic data are barely available. This is to a large degree because of the complexity of GCS, which is composed of four proteins (H, T, P, and L) and catalyzes reactions involving different substrates and cofactors. In vitro kinetics of reconstructed microbial multi-enzyme glycine cleavage/synthase system is desired to better implement rGlyP in microorganisms like Escherichia coli for the use of C1 resources. Here, we examined in vitro several factors that may affect the rate of glycine synthesis via the reverse GCS reaction. We found that the ratio of GCS component proteins has a direct influence on the rate of glycine synthesis, namely higher ratios of P protein and especially H protein to T and L proteins are favorable, and the carboxylation reaction catalyzed by P protein is a key step determining the glycine synthesis rate, whereas increasing the ratio of L protein to other GCS proteins does not have significant effect and the ratio of T protein to other GCS proteins should be kept low. The effect of substrate concentrations on glycine synthesis is quite complex, showing interdependence with the ratios of GCS component proteins. Furthermore, adding the reducing agent dithiothreitol to the reaction mixture not only results in great tolerance to high concentration of formaldehyde, but also increases the rate of glycine synthesis, probably due to its functions in activating P protein and taking up the role of L protein in the non-enzymatic reduction of Hox to Hred. Moreover, the presence of some monovalent and divalent metal ions can have either positive or negative effect on the rate of glycine synthesis, depending on their type and their concentration.
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Affiliation(s)
- Yingying Xu
- Beijing Advanced Innovation Center for Soft Matter Science and EngineeringBeijing University of Chemical TechnologyBeijingP. R. China
| | - Jie Ren
- Beijing Advanced Innovation Center for Soft Matter Science and EngineeringBeijing University of Chemical TechnologyBeijingP. R. China
- State Key Laboratory for Biology of Plant Diseases and Insect Pests/Key Laboratory of Control of Biological Hazard Factors (Plant Origin) for Agri‐product Quality and SafetyMinistry of AgricultureInstitute of Plant ProtectionChinese Academy of Agricultural SciencesBeijingP. R. China
| | - Wei Wang
- Institute of Bioprocess and Biosystems Engineering, Hamburg University of TechnologyHamburgGermany
| | - An‐Ping Zeng
- Beijing Advanced Innovation Center for Soft Matter Science and EngineeringBeijing University of Chemical TechnologyBeijingP. R. China
- Institute of Bioprocess and Biosystems Engineering, Hamburg University of TechnologyHamburgGermany
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Kang X, Yuan D, Yi Z, Yu C, Yuan X, Liang B, San X, Gao L, Wang S, Li Y. Bismuth single atom supported CeO 2 nanosheets for oxidation resistant photothermal reverse water gas shift reaction. Catal Sci Technol 2022. [DOI: 10.1039/d2cy00771a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Bi single atoms supported on CeO2 nanosheets combined with a Ti2O3 based photothermal device showed oxidation resistance and outperforming weak solar driven RWGS with a CO production rate of 31.00 mmol g−1 h−1 under 3 sun units of irradiation.
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Affiliation(s)
- Xiaoxiao Kang
- Hebei Key Lab of Optic-electronic Information and Materials, The College of Physics Science and Technology, Institute of Life Science and Green Development, Hebei University, Baoding, 071002, China
| | - Dachao Yuan
- College of Mechanical and Electrical Engineering, Hebei Agricultural University, Baoding 071001, P. R. China
| | - Zhiqi Yi
- Hebei Key Lab of Optic-electronic Information and Materials, The College of Physics Science and Technology, Institute of Life Science and Green Development, Hebei University, Baoding, 071002, China
| | - Chenyang Yu
- Hebei Key Lab of Optic-electronic Information and Materials, The College of Physics Science and Technology, Institute of Life Science and Green Development, Hebei University, Baoding, 071002, China
| | - Xiaoxian Yuan
- Hebei Key Lab of Optic-electronic Information and Materials, The College of Physics Science and Technology, Institute of Life Science and Green Development, Hebei University, Baoding, 071002, China
| | - Baolai Liang
- Hebei Key Lab of Optic-electronic Information and Materials, The College of Physics Science and Technology, Institute of Life Science and Green Development, Hebei University, Baoding, 071002, China
| | - Xingyuan San
- Hebei Key Lab of Optic-electronic Information and Materials, The College of Physics Science and Technology, Institute of Life Science and Green Development, Hebei University, Baoding, 071002, China
| | - Linjie Gao
- Hebei Key Lab of Optic-electronic Information and Materials, The College of Physics Science and Technology, Institute of Life Science and Green Development, Hebei University, Baoding, 071002, China
| | - Shufang Wang
- Hebei Key Lab of Optic-electronic Information and Materials, The College of Physics Science and Technology, Institute of Life Science and Green Development, Hebei University, Baoding, 071002, China
| | - Yaguang Li
- Hebei Key Lab of Optic-electronic Information and Materials, The College of Physics Science and Technology, Institute of Life Science and Green Development, Hebei University, Baoding, 071002, China
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Wimmer JLE, Xavier JC, Vieira ADN, Pereira DPH, Leidner J, Sousa FL, Kleinermanns K, Preiner M, Martin WF. Energy at Origins: Favorable Thermodynamics of Biosynthetic Reactions in the Last Universal Common Ancestor (LUCA). Front Microbiol 2021; 12:793664. [PMID: 34966373 PMCID: PMC8710812 DOI: 10.3389/fmicb.2021.793664] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 11/24/2021] [Indexed: 12/02/2022] Open
Abstract
Though all theories for the origin of life require a source of energy to promote primordial chemical reactions, the nature of energy that drove the emergence of metabolism at origins is still debated. We reasoned that evidence for the nature of energy at origins should be preserved in the biochemical reactions of life itself, whereby changes in free energy, ΔG, which determine whether a reaction can go forward or not, should help specify the source. By calculating values of ΔG across the conserved and universal core of 402 individual reactions that synthesize amino acids, nucleotides and cofactors from H2, CO2, NH3, H2S and phosphate in modern cells, we find that 95-97% of these reactions are exergonic (ΔG ≤ 0 kJ⋅mol-1) at pH 7-10 and 80-100°C under nonequilibrium conditions with H2 replacing biochemical reductants. While 23% of the core's reactions involve ATP hydrolysis, 77% are ATP-independent, thermodynamically driven by ΔG of reactions involving carbon bonds. We identified 174 reactions that are exergonic by -20 to -300 kJ⋅mol-1 at pH 9 and 80°C and that fall into ten reaction types: six pterin dependent alkyl or acyl transfers, ten S-adenosylmethionine dependent alkyl transfers, four acyl phosphate hydrolyses, 14 thioester hydrolyses, 30 decarboxylations, 35 ring closure reactions, 31 aromatic ring formations, and 44 carbon reductions by reduced nicotinamide, flavins, ferredoxin, or formate. The 402 reactions of the biosynthetic core trace to the last universal common ancestor (LUCA), and reveal that synthesis of LUCA's chemical constituents required no external energy inputs such as electric discharge, UV-light or phosphide minerals. The biosynthetic reactions of LUCA uncover a natural thermodynamic tendency of metabolism to unfold from energy released by reactions of H2, CO2, NH3, H2S, and phosphate.
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Affiliation(s)
- Jessica L. E. Wimmer
- Department of Biology, Institute of Molecular Evolution, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Joana C. Xavier
- Department of Biology, Institute of Molecular Evolution, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Andrey d. N. Vieira
- Department of Biology, Institute of Molecular Evolution, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Delfina P. H. Pereira
- Department of Biology, Institute of Molecular Evolution, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Jacqueline Leidner
- Department of Biology, Institute of Molecular Evolution, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Filipa L. Sousa
- Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | - Karl Kleinermanns
- Department of Chemistry, Institute of Physical Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Martina Preiner
- Department of Biology, Institute of Molecular Evolution, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - William F. Martin
- Department of Biology, Institute of Molecular Evolution, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
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Kang W, Suzuki M, Saito T, Miyado K. Emerging Role of TCA Cycle-Related Enzymes in Human Diseases. Int J Mol Sci 2021; 22:13057. [PMID: 34884868 PMCID: PMC8657694 DOI: 10.3390/ijms222313057] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 11/27/2021] [Accepted: 11/30/2021] [Indexed: 02/03/2023] Open
Abstract
The tricarboxylic acid (TCA) cycle is the main source of cellular energy and participates in many metabolic pathways in cells. Recent reports indicate that dysfunction of TCA cycle-related enzymes causes human diseases, such as neurometabolic disorders and tumors, have attracted increasing interest in their unexplained roles. The diseases which develop as a consequence of loss or dysfunction of TCA cycle-related enzymes are distinct, suggesting that each enzyme has a unique function. This review aims to provide a comprehensive overview of the relationship between each TCA cycle-related enzyme and human diseases. We also discuss their functions in the context of both mitochondrial and extra-mitochondrial (or cytoplasmic) enzymes.
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Affiliation(s)
- Woojin Kang
- Department of Reproductive Biology, National Research Institute for Child Health and Development, Tokyo 157-8535, Japan; (M.S.); (K.M.)
| | - Miki Suzuki
- Department of Reproductive Biology, National Research Institute for Child Health and Development, Tokyo 157-8535, Japan; (M.S.); (K.M.)
| | - Takako Saito
- Department of Applied Life Sciences, Faculty of Agriculture, Shizuoka University, Shizuoka 422-8529, Japan;
| | - Kenji Miyado
- Department of Reproductive Biology, National Research Institute for Child Health and Development, Tokyo 157-8535, Japan; (M.S.); (K.M.)
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The existence of a nonclassical TCA cycle in the nucleus that wires the metabolic-epigenetic circuitry. Signal Transduct Target Ther 2021; 6:375. [PMID: 34728602 PMCID: PMC8563883 DOI: 10.1038/s41392-021-00774-2] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 09/12/2021] [Accepted: 09/15/2021] [Indexed: 12/12/2022] Open
Abstract
The scope and variety of the metabolic intermediates from the mitochondrial tricarboxylic acid (TCA) cycle that are engaged in epigenetic regulation of the chromatin function in the nucleus raise an outstanding question about how timely and precise supply/consumption of these metabolites is achieved in the nucleus. We report here the identification of a nonclassical TCA cycle in the nucleus (nTCA cycle). We found that all the TCA cycle-associated enzymes including citrate synthase (CS), aconitase 2 (ACO2), isocitrate dehydrogenase 3 (IDH3), oxoglutarate dehydrogenase (OGDH), succinyl-CoA synthetase (SCS), fumarate hydratase (FH), and malate dehydrogenase 2 (MDH2), except for succinate dehydrogenase (SDH), a component of electron transport chain for generating ATP, exist in the nucleus. We showed that these nuclear enzymes catalyze an incomplete TCA cycle similar to that found in cyanobacteria. We propose that the nTCA cycle is implemented mainly to generate/consume metabolic intermediates, not for energy production. We demonstrated that the nTCA cycle is intrinsically linked to chromatin dynamics and transcription regulation. Together, our study uncovers the existence of a nonclassical TCA cycle in the nucleus that links the metabolic pathway to epigenetic regulation.
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Sumi T, Harada K. Kinetics of the ancestral carbon metabolism pathways in deep-branching bacteria and archaea. Commun Chem 2021; 4:149. [PMID: 36697601 PMCID: PMC9814661 DOI: 10.1038/s42004-021-00585-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 10/04/2021] [Indexed: 01/28/2023] Open
Abstract
The origin of life is believed to be chemoautotrophic, deriving all biomass components from carbon dioxide, and all energy from inorganic redox couples in the environment. The reductive tricarboxylic acid cycle (rTCA) and the Wood-Ljungdahl pathway (WL) have been recognized as the most ancient carbon fixation pathways. The rTCA of the chemolithotrophic Thermosulfidibacter takaii, which was recently demonstrated to take place via an unexpected reverse reaction of citrate synthase, was reproduced using a kinetic network model, and a competition between reductive and oxidative fluxes on rTCA due to an acetyl coenzyme A (ACOA) influx upon acetate uptake was revealed. Avoiding ACOA direct influx into rTCA from WL is, therefore, raised as a kinetically necessary condition to maintain a complete rTCA. This hypothesis was confirmed for deep-branching bacteria and archaea, and explains the kinetic factors governing elementary processes in carbon metabolism evolution from the last universal common ancestor.
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Affiliation(s)
- Tomonari Sumi
- Research Institute for Interdisciplinary Science, Okayama University, 3-1-1 Tsushima-Naka, Kita-ku, Okayama, 700-8530, Japan. .,Department of Chemistry, Faculty of Science, Okayama University, 3-1-1 Tsushima-Naka, Kita-ku, Okayama, 700-8530, Japan.
| | - Kouji Harada
- Department of Computer Science and Engineering, Toyohashi University of Technology, Tempaku-cho, Toyohashi, 441-8580, Japan.,Center for IT-Based Education, Toyohashi University of Technology, Tempaku-cho, Toyohashi, Aichi, 441-8580, Japan
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Harnessing Escherichia coli for Bio-Based Production of Formate under Pressurized H 2 and CO 2 Gases. Appl Environ Microbiol 2021; 87:e0029921. [PMID: 34647819 DOI: 10.1128/aem.00299-21] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Escherichia coli is a Gram-negative bacterium that is a workhorse for biotechnology. The organism naturally performs a mixed-acid fermentation under anaerobic conditions where it synthesizes formate hydrogenlyase (FHL-1). The physiological role of the enzyme is the disproportionation of formate into H2 and CO2. However, the enzyme has been observed to catalyze hydrogenation of CO2 given the correct conditions, and so it has possibilities in bio-based carbon capture and storage if it can be harnessed as a hydrogen-dependent CO2 reductase (HDCR). In this study, an E. coli host strain was engineered for the continuous production of formic acid from H2 and CO2 during bacterial growth in a pressurized batch bioreactor. Incorporation of tungsten, in place of molybdenum, in FHL-1 helped to impose a degree of catalytic bias on the enzyme. This work demonstrates that it is possible to couple cell growth to simultaneous, unidirectional formate production from carbon dioxide and develops a process for growth under pressurized gases. IMPORTANCE Greenhouse gas emissions, including waste carbon dioxide, are contributing to global climate change. A basket of solutions is needed to steadily reduce emissions, and one approach is bio-based carbon capture and storage. Here, we present our latest work on harnessing a novel biological solution for carbon capture. The Escherichia coli formate hydrogenlyase (FHL-1) was engineered to be constitutively expressed. Anaerobic growth under pressurized H2 and CO2 gases was established, and aqueous formic acid was produced as a result. Incorporation of tungsten into the enzyme in place of molybdenum proved useful in poising FHL-1 as a hydrogen-dependent CO2 reductase (HDCR).
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Cooccurring Activities of Two Autotrophic Pathways in Symbionts of the Hydrothermal Vent Tubeworm Riftia pachyptila. Appl Environ Microbiol 2021; 87:e0079421. [PMID: 34190607 DOI: 10.1128/aem.00794-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Genome and proteome data predict the presence of both the reductive citric acid cycle (rCAC; also called the reductive tricarboxylic acid cycle) and the Calvin-Benson-Bassham cycle (CBB) in "Candidatus Endoriftia persephonae," the autotrophic sulfur-oxidizing bacterial endosymbiont from the giant hydrothermal vent tubeworm Riftia pachyptila. We tested whether these cycles were differentially induced by sulfide supply, since the synthesis of biosynthetic intermediates by the rCAC is less energetically expensive than that by the CBB. R. pachyptila was incubated under in situ conditions in high-pressure aquaria under low (28 to 40 μmol · h-1) or high (180 to 276 μmol · h-1) rates of sulfide supply. Symbiont-bearing trophosome samples excised from R. pachyptila maintained under the two conditions were capable of similar rates of CO2 fixation. Activities of the rCAC enzyme ATP-dependent citrate lyase (ACL) and the CBB enzyme 1,3-bisphosphate carboxylase/oxygenase (RubisCO) did not differ between the two conditions, although transcript abundances for ATP-dependent citrate lyase were 4- to 5-fold higher under low-sulfide conditions. δ13C values of internal dissolved inorganic carbon (DIC) pools were varied and did not correlate with sulfide supply rate. In samples taken from freshly collected R. pachyptila, δ13C values of lipids fell between those collected for organisms using either the rCAC or the CBB exclusively. These observations are consistent with cooccurring activities of the rCAC and the CBB in this symbiosis. IMPORTANCE Previous to this study, the activities of the rCAC and CBB in R. pachyptila had largely been inferred from "omics" studies of R. pachyptila without direct assessment of in situ conditions prior to collection. In this study, R. pachyptila was maintained and monitored in high-pressure aquaria prior to measuring its CO2 fixation parameters. Results suggest that ranges in sulfide concentrations similar to those experienced in situ do not exert a strong influence on the relative activities of the rCAC and the CBB. This observation highlights the importance of further study of this symbiosis and other organisms with multiple CO2-fixing pathways, which recent genomics and biochemical studies suggest are likely to be more prevalent than anticipated.
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York A. Adapting to high levels of CO 2. Nat Rev Microbiol 2021; 19:405. [PMID: 33953360 DOI: 10.1038/s41579-021-00571-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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