1
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Heffernan J, Garcia Gonzalez RA, Mahamkali V, McCubbin T, Daygon D, Liu L, Palfreyman R, Harris A, Koepke M, Valgepea K, Nielsen LK, Marcellin E. Adaptive laboratory evolution of Clostridium autoethanogenum to metabolize CO 2 and H 2 enhances growth rates in chemostat and unravels proteome and metabolome alterations. Microb Biotechnol 2024; 17:e14452. [PMID: 38568755 PMCID: PMC10990044 DOI: 10.1111/1751-7915.14452] [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: 08/17/2023] [Revised: 03/03/2024] [Accepted: 03/06/2024] [Indexed: 04/05/2024] Open
Abstract
Gas fermentation of CO2 and H2 is an attractive means to sustainably produce fuels and chemicals. Clostridium autoethanogenum is a model organism for industrial CO to ethanol and presents an opportunity for CO2-to-ethanol processes. As we have previously characterized its CO2/H2 chemostat growth, here we use adaptive laboratory evolution (ALE) with the aim of improving growth with CO2/H2. Seven ALE lineages were generated, all with improved specific growth rates. ALE conducted in the presence of 2% CO along with CO2/H2 generated Evolved lineage D, which showed the highest ethanol titres amongst all the ALE lineages during the fermentation of CO2/H2. Chemostat comparison against the parental strain shows no change in acetate or ethanol production, while Evolved D could achieve a higher maximum dilution rate. Multi-omics analyses at steady state revealed that Evolved D has widespread proteome and intracellular metabolome changes. However, the uptake and production rates and titres remain unaltered until investigating their maximum dilution rate. Yet, we provide numerous insights into CO2/H2 metabolism via these multi-omics data and link these results to mutations, suggesting novel targets for metabolic engineering in this bacterium.
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Affiliation(s)
- James Heffernan
- Australian Institute of Bioengineering and NanotechnologyThe University of QueenslandSt. LuciaQueenslandAustralia
- ARC Centre of Excellence in Synthetic BiologyThe University of QueenslandSt. LuciaQueenslandAustralia
| | - R. Axayactl Garcia Gonzalez
- Australian Institute of Bioengineering and NanotechnologyThe University of QueenslandSt. LuciaQueenslandAustralia
- ARC Centre of Excellence in Synthetic BiologyThe University of QueenslandSt. LuciaQueenslandAustralia
| | | | - Tim McCubbin
- Queensland Metabolomics and Proteomics Q‐MAPThe University of QueenslandSt. LuciaQueenslandAustralia
| | - Dara Daygon
- Queensland Metabolomics and Proteomics Q‐MAPThe University of QueenslandSt. LuciaQueenslandAustralia
| | - Lian Liu
- Queensland Metabolomics and Proteomics Q‐MAPThe University of QueenslandSt. LuciaQueenslandAustralia
| | - Robin Palfreyman
- Queensland Metabolomics and Proteomics Q‐MAPThe University of QueenslandSt. LuciaQueenslandAustralia
| | | | | | - Kaspar Valgepea
- ERA Chair in Gas Fermentation Technologies, Institute of TechnologyUniversity of TartuTartuEstonia
| | - Lars Keld Nielsen
- Australian Institute of Bioengineering and NanotechnologyThe University of QueenslandSt. LuciaQueenslandAustralia
- ARC Centre of Excellence in Synthetic BiologyThe University of QueenslandSt. LuciaQueenslandAustralia
- Queensland Metabolomics and Proteomics Q‐MAPThe University of QueenslandSt. LuciaQueenslandAustralia
- The Novo Nordisk Foundation Center for BiosustainabilityTechnical University of DenmarkKgs. LyngbyDenmark
| | - Esteban Marcellin
- Australian Institute of Bioengineering and NanotechnologyThe University of QueenslandSt. LuciaQueenslandAustralia
- ARC Centre of Excellence in Synthetic BiologyThe University of QueenslandSt. LuciaQueenslandAustralia
- Queensland Metabolomics and Proteomics Q‐MAPThe University of QueenslandSt. LuciaQueenslandAustralia
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2
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Kurt E, Qin J, Williams A, Zhao Y, Xie D. Perspectives for Using CO 2 as a Feedstock for Biomanufacturing of Fuels and Chemicals. Bioengineering (Basel) 2023; 10:1357. [PMID: 38135948 PMCID: PMC10740661 DOI: 10.3390/bioengineering10121357] [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: 10/17/2023] [Revised: 11/20/2023] [Accepted: 11/24/2023] [Indexed: 12/24/2023] Open
Abstract
Microbial cell factories offer an eco-friendly alternative for transforming raw materials into commercially valuable products because of their reduced carbon impact compared to conventional industrial procedures. These systems often depend on lignocellulosic feedstocks, mainly pentose and hexose sugars. One major hurdle when utilizing these sugars, especially glucose, is balancing carbon allocation to satisfy energy, cofactor, and other essential component needs for cellular proliferation while maintaining a robust yield. Nearly half or more of this carbon is inevitably lost as CO2 during the biosynthesis of regular metabolic necessities. This loss lowers the production yield and compromises the benefit of reducing greenhouse gas emissions-a fundamental advantage of biomanufacturing. This review paper posits the perspectives of using CO2 from the atmosphere, industrial wastes, or the exhausted gases generated in microbial fermentation as a feedstock for biomanufacturing. Achieving the carbon-neutral or -negative goals is addressed under two main strategies. The one-step strategy uses novel metabolic pathway design and engineering approaches to directly fix the CO2 toward the synthesis of the desired products. Due to the limitation of the yield and efficiency in one-step fixation, the two-step strategy aims to integrate firstly the electrochemical conversion of the exhausted CO2 into C1/C2 products such as formate, methanol, acetate, and ethanol, and a second fermentation process to utilize the CO2-derived C1/C2 chemicals or co-utilize C5/C6 sugars and C1/C2 chemicals for product formation. The potential and challenges of using CO2 as a feedstock for future biomanufacturing of fuels and chemicals are also discussed.
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Affiliation(s)
- Elif Kurt
- Department of Chemical Engineering, University of Massachusetts, Lowell, MA 01854, USA; (E.K.); (J.Q.); (A.W.)
| | - Jiansong Qin
- Department of Chemical Engineering, University of Massachusetts, Lowell, MA 01854, USA; (E.K.); (J.Q.); (A.W.)
| | - Alexandria Williams
- Department of Chemical Engineering, University of Massachusetts, Lowell, MA 01854, USA; (E.K.); (J.Q.); (A.W.)
| | - Youbo Zhao
- Physical Sciences Inc., 20 New England Business Ctr., Andover, MA 01810, USA;
| | - Dongming Xie
- Department of Chemical Engineering, University of Massachusetts, Lowell, MA 01854, USA; (E.K.); (J.Q.); (A.W.)
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3
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Jia D, Deng W, Hu P, Jiang W, Gu Y. Thermophilic Moorella thermoacetica as a platform microorganism for C1 gas utilization: physiology, engineering, and applications. BIORESOUR BIOPROCESS 2023; 10:61. [PMID: 38647965 PMCID: PMC10992200 DOI: 10.1186/s40643-023-00682-z] [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: 06/27/2023] [Accepted: 08/29/2023] [Indexed: 04/25/2024] Open
Abstract
In the context of the rapid development of low-carbon economy, there has been increasing interest in utilizing naturally abundant and cost-effective one-carbon (C1) substrates for sustainable production of chemicals and fuels. Moorella thermoacetica, a model acetogenic bacterium, has attracted significant attention due to its ability to utilize carbon dioxide (CO2) and carbon monoxide (CO) via the Wood-Ljungdahl (WL) pathway, thereby showing great potential for the utilization of C1 gases. However, natural strains of M. thermoacetica are not yet fully suitable for industrial applications due to their limitations in carbon assimilation and conversion efficiency as well as limited product range. Over the past decade, progresses have been made in the development of genetic tools for M. thermoacetica, accelerating the understanding and modification of this acetogen. Here, we summarize the physiological and metabolic characteristics of M. thermoacetica and review the recent advances in engineering this bacterium. Finally, we propose the future directions for exploring the real potential of M. thermoacetica in industrial applications.
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Affiliation(s)
- Dechen Jia
- 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
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wangshuying Deng
- 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
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Peng Hu
- Shanghai GTLB Biotech Co., Ltd, 1688 North Guoquan Road, Shanghai, 200438, China
| | - Weihong Jiang
- 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
| | - Yang Gu
- 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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4
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Hocq R, Bottone S, Gautier A, Pflügl S. A fluorescent reporter system for anaerobic thermophiles. Front Bioeng Biotechnol 2023; 11:1226889. [PMID: 37476481 PMCID: PMC10355840 DOI: 10.3389/fbioe.2023.1226889] [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: 05/22/2023] [Accepted: 06/23/2023] [Indexed: 07/22/2023] Open
Abstract
Owing to their inherent capacity to make invisible biological processes visible and quantifiable, fluorescent reporter systems have numerous applications in biotechnology. For classical fluorescent protein systems (i.e., GFP and derivatives), chromophore maturation is O2-dependent, restricting their applications to aerobic organisms. In this work, we pioneered the use of the oxygen-independent system FAST (Fluorescence Activating and absorption Shifting tag) in the thermophilic anaerobe Thermoanaerobacter kivui. We developed a modular cloning system that was used to easily clone a library of FAST expression cassettes in an E. coli-Thermoanaerobacter shuttle plasmid. FAST-mediated fluorescence was then assessed in vivo in T. kivui, and we observed bright green and red fluorescence for cells grown at 55°C. Next, we took advantage of this functional reporter system to characterize a set of homologous and heterologous promoters by quantifying gene expression, expanding the T. kivui genetic toolbox. Low fluorescence at 66°C (Topt for T. kivui) was subsequently investigated at the single-cell level using flow cytometry and attributed to plasmid instability at higher temperatures. Adaptive laboratory evolution circumvented this issue and drastically enhanced fluorescence at 66°C. Whole plasmid sequencing revealed the evolved strain carried functional plasmids truncated at the Gram-positive origin of replication, that could however not be linked to the increased fluorescence displayed by the evolved strain. Collectively, our work demonstrates the applicability of the FAST fluorescent reporter systems to T. kivui, paving the way for further applications in thermophilic anaerobes.
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Affiliation(s)
- Rémi Hocq
- Institute of Chemical, Environmental and Bioscience Engineering, Technische Universität Wien, Vienna, Austria
- Christian Doppler Laboratory for Optimized Expression of Carbohydrate-Active Enzymes, Institute of Chemical, Environmental and Bioscience Engineering, Technische Universität Wien, Vienna, Austria
| | - Sara Bottone
- Laboratoire des Biomolécules (LBM), Centre National de la Recherche Scientifique (CNRS), Sorbonne Université, École Normale Supérieure, Université PSL, Paris, France
- Institut Universitaire de France, Paris, France
| | - Arnaud Gautier
- Laboratoire des Biomolécules (LBM), Centre National de la Recherche Scientifique (CNRS), Sorbonne Université, École Normale Supérieure, Université PSL, Paris, France
- Institut Universitaire de France, Paris, France
| | - Stefan Pflügl
- Institute of Chemical, Environmental and Bioscience Engineering, Technische Universität Wien, Vienna, Austria
- Christian Doppler Laboratory for Optimized Expression of Carbohydrate-Active Enzymes, Institute of Chemical, Environmental and Bioscience Engineering, Technische Universität Wien, Vienna, Austria
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5
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Wood JC, Gonzalez-Garcia RA, Daygon D, Talbo G, Plan MR, Marcellin E, Virdis B. Characterisation of acetogen formatotrophic potential using Eubacterium limosum. Appl Microbiol Biotechnol 2023:10.1007/s00253-023-12600-6. [PMID: 37272938 DOI: 10.1007/s00253-023-12600-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 05/09/2023] [Accepted: 05/14/2023] [Indexed: 06/06/2023]
Abstract
Formate is a promising energy carrier that could be used to transport renewable electricity. Some acetogenic bacteria, such as Eubacterium limosum, have the native ability to utilise formate as a sole substrate for growth, which has sparked interest in the biotechnology industry. However, formatotrophic metabolism in E. limosum is poorly understood, and a system-level characterisation in continuous cultures is yet to be reported. Here, we present the first steady-state dataset for E. limosum formatotrophic growth. At a defined dilution rate of 0.4 d-1, there was a high specific uptake rate of formate (280 ± 56 mmol/gDCW/d; gDCW = gramme dry cell weight); however, most carbon went to CO2 (150 ± 11 mmol/gDCW/d). Compared to methylotrophic growth, protein differential expression data and intracellular metabolomics revealed several key features of formate metabolism. Upregulation of phosphotransacetylase (Pta) appears to be a futile attempt of cells to produce acetate as the major product. Instead, a cellular energy limitation resulted in the accumulation of intracellular pyruvate and upregulation of pyruvate formate ligase (Pfl) to convert formate to pyruvate. Therefore, metabolism is controlled, at least partially, at the protein expression level, an unusual feature for an acetogen. We anticipate that formate could be an important one-carbon substrate for acetogens to produce chemicals rich in pyruvate, a metabolite generally in low abundance during syngas growth. KEY POINTS: First Eubacterium limosum steady-state formatotrophic growth omics dataset High formate specific uptake rate, however carbon dioxide was the major product Formate may be the cause of intracellular stress and biofilm formation.
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Affiliation(s)
- Jamin C Wood
- Australian Centre for Water and Environmental Biotechnology (ACWEB), The University of Queensland, QLD, Brisbane, 4072, Australia
| | - R Axayacatl Gonzalez-Garcia
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, QLD, Brisbane, 4072, Australia
| | - Dara Daygon
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, QLD, Brisbane, 4072, Australia
- Metabolomics Australia (Queensland Node), The University of Queensland, QLD, Brisbane, 4072, Australia
| | - Gert Talbo
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, QLD, Brisbane, 4072, Australia
- Metabolomics Australia (Queensland Node), The University of Queensland, QLD, Brisbane, 4072, Australia
| | - Manuel R Plan
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, QLD, Brisbane, 4072, Australia
- Metabolomics Australia (Queensland Node), The University of Queensland, QLD, Brisbane, 4072, Australia
| | - Esteban Marcellin
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, QLD, Brisbane, 4072, Australia
- Metabolomics Australia (Queensland Node), The University of Queensland, QLD, Brisbane, 4072, Australia
| | - Bernardino Virdis
- Australian Centre for Water and Environmental Biotechnology (ACWEB), The University of Queensland, QLD, Brisbane, 4072, Australia.
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6
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Suda K, Sakamoto S, Iguchi A, Tamaki H. Novel quantitative method for individual isotopomer of organic acids from 13C tracer experiments determines carbon flow in acetogenesis. Talanta 2023; 257:124328. [PMID: 36801560 DOI: 10.1016/j.talanta.2023.124328] [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: 08/09/2022] [Revised: 01/04/2023] [Accepted: 02/04/2023] [Indexed: 02/10/2023]
Abstract
Anaerobic microbial acetogenesis is ubiquitous on Earth, and thus plays an important role in the global carbon cycle. The mechanism of carbon fixation in acetogens has attracted great interest from various studies for combatting climate change, and even for studying ancient metabolic pathways. Here, we developed a new, simple method for investigating carbon flows in the metabolic reaction of acetogen by conveniently and accurately determining the relative abundance of individual acetate- and/or formate-isotopomers formed in 13C labeling experiments. We measured the underivatized analyte by gas chromatography-mass spectrometry (GC-MS) coupled with a direct aqueous sample injection technique. The individual abundance of analyte isotopomers was calculated by the mass spectrum analysis using the least-squares approach. The validity of the method was demonstrated by determining known mixtures of unlabeled and 13C-labeled analytes. The developed method was applied to study the carbon fixation mechanism of the well-known acetogen Acetobacterium woodii grown on methanol and bicarbonate. We provided a quantitative reaction model for methanol metabolism of A. woodii, which indicated that methanol was not the sole carbon precursor of the acetate methyl group and that 20-22% of the methyl group was formed from CO2. In contrast, the carboxyl group of acetate appeared to form exclusively by CO2 fixation. Thus, our simple method, without laborious analytical procedures, has broad utility for the study of biochemical and chemical processes related to acetogenesis on Earth.
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Affiliation(s)
- Konomi Suda
- Geological Survey of Japan, National Institute of Advanced Industrial Science and Technology (AIST), Central 7, 1-1-1 Higashi, Tsukuba, Ibaraki, 305-8567, Japan.
| | - Sachiko Sakamoto
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki, 305-8566, Japan
| | - Akira Iguchi
- Geological Survey of Japan, National Institute of Advanced Industrial Science and Technology (AIST), Central 7, 1-1-1 Higashi, Tsukuba, Ibaraki, 305-8567, Japan
| | - Hideyuki Tamaki
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki, 305-8566, Japan
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7
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Xu J, Wang J, Ma C, Wei Z, Zhai Y, Tian N, Zhu Z, Xue M, Li D. Embracing a low-carbon future by the production and marketing of C1 gas protein. Biotechnol Adv 2023; 63:108096. [PMID: 36621726 DOI: 10.1016/j.biotechadv.2023.108096] [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: 08/29/2022] [Revised: 12/14/2022] [Accepted: 01/03/2023] [Indexed: 01/07/2023]
Abstract
Food scarcity and environmental deterioration are two major problems that human populations currently face. Fortunately, the disruptive innovation of raw food materials has been stimulated by the rapid evolution of biomanufacturing. Therefore, it is expected that the new trends in technology will not only alter the natural resource-dependent food production systems and the traditional way of life but also reduce and assimilate the greenhouse gases released into the atmosphere. This review article summarizes the metabolic pathways associated with C1 gas conversion and the production of single-cell protein for animal feed. Moreover, the protein function, worldwide authorization, market access, and methods to overcome challenges in C1 gas assimilation microbial cell factory construction are also provided. With widespread attention and increasing policy support, the production of C1 gas protein will bring more opportunities and make tremendous contributions to our sustainable future.
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Affiliation(s)
- Jian Xu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China; National Centre of Technology Innovation for Synthetic Biology, Tianjin, China; Tianjin Key Laboratory for Industrial Biological Systems and Bioprocessing Engineering, Tianjin, China
| | - Jie Wang
- Institute of Feed Research, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Chunling Ma
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China; Haihe Laboratory of Synthetic Biology, Tianjin, China; National Centre of Technology Innovation for Synthetic Biology, Tianjin, China
| | - Zuoxi Wei
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China; National Centre of Technology Innovation for Synthetic Biology, Tianjin, China; Tianjin Key Laboratory for Industrial Biological Systems and Bioprocessing Engineering, Tianjin, China
| | - Yida Zhai
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China; National Centre of Technology Innovation for Synthetic Biology, Tianjin, China; Tianjin Key Laboratory for Industrial Biological Systems and Bioprocessing Engineering, Tianjin, China
| | - Na Tian
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China; National Centre of Technology Innovation for Synthetic Biology, Tianjin, China; Tianjin Key Laboratory for Industrial Biological Systems and Bioprocessing Engineering, Tianjin, China
| | - Zhiguang Zhu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China; National Centre of Technology Innovation for Synthetic Biology, Tianjin, China.
| | - Min Xue
- Institute of Feed Research, Chinese Academy of Agricultural Sciences, Beijing, China.
| | - Demao Li
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China; National Centre of Technology Innovation for Synthetic Biology, Tianjin, China; Tianjin Key Laboratory for Industrial Biological Systems and Bioprocessing Engineering, Tianjin, China.
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8
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Improving glycine utilization in Escherichia coli. Biochem Eng J 2023. [DOI: 10.1016/j.bej.2023.108834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
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9
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Stark C, Münßinger S, Rosenau F, Eikmanns BJ, Schwentner A. The Potential of Sequential Fermentations in Converting C1 Substrates to Higher-Value Products. Front Microbiol 2022; 13:907577. [PMID: 35722332 PMCID: PMC9204031 DOI: 10.3389/fmicb.2022.907577] [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: 03/29/2022] [Accepted: 05/18/2022] [Indexed: 11/13/2022] Open
Abstract
Today production of (bulk) chemicals and fuels almost exclusively relies on petroleum-based sources, which are connected to greenhouse gas release, fueling climate change. This increases the urgence to develop alternative bio-based technologies and processes. Gaseous and liquid C1 compounds are available at low cost and often occur as waste streams. Acetogenic bacteria can directly use C1 compounds like CO, CO2, formate or methanol anaerobically, converting them into acetate and ethanol for higher-value biotechnological products. However, these microorganisms possess strict energetic limitations, which in turn pose limitations to their potential for biotechnological applications. Moreover, efficient genetic tools for strain improvement are often missing. However, focusing on the metabolic abilities acetogens provide, they can prodigiously ease these technological disadvantages. Producing acetate and ethanol from C1 compounds can fuel via bio-based intermediates conversion into more energy-demanding, higher-value products, by deploying aerobic organisms that are able to grow with acetate/ethanol as carbon and energy source. Promising new approaches have become available combining these two fermentation steps in sequential approaches, either as separate fermentations or as integrated two-stage fermentation processes. This review aims at introducing, comparing, and evaluating the published approaches of sequential C1 fermentations, delivering a list of promising organisms for the individual fermentation steps and giving an overview of the existing broad spectrum of products based on acetate and ethanol. Understanding of these pioneering approaches allows collecting ideas for new products and may open avenues toward making full use of the technological potential of these concepts for establishment of a sustainable biotechnology.
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Affiliation(s)
- Christina Stark
- Institute of Microbiology and Biotechnology, University of Ulm, Ulm, Germany
| | - Sini Münßinger
- Institute of Microbiology and Biotechnology, University of Ulm, Ulm, Germany
| | - Frank Rosenau
- Institute of Pharmaceutical Biotechnology, University of Ulm, Ulm, Germany
| | - Bernhard J. Eikmanns
- Institute of Microbiology and Biotechnology, University of Ulm, Ulm, Germany
- *Correspondence: Bernhard J. Eikmanns,
| | - Andreas Schwentner
- Institute of Microbiology and Biotechnology, University of Ulm, Ulm, Germany
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10
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Vees CA, Herwig C, Pflügl S. Mixotrophic co-utilization of glucose and carbon monoxide boosts ethanol and butanol productivity of continuous Clostridium carboxidivorans cultures. BIORESOURCE TECHNOLOGY 2022; 353:127138. [PMID: 35405210 DOI: 10.1016/j.biortech.2022.127138] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 04/05/2022] [Accepted: 04/06/2022] [Indexed: 06/14/2023]
Abstract
In this study, continuous cultivations of C.carboxidivorans to study heterotrophic and mixotrophic conversion of glucose and H2, CO2, and CO were established. Glucose fermentations at pH 6 showed a high ratio of alcohol-to-acid production of 2.79 mol mol-1. While H2 or CO2 were not utilized together with glucose, CO feeding drastically increased the combined alcohol titer to 9.1 g l-1. Specifically, CO enhanced acetate (1.9-fold) and ethanol (1.7-fold) production and triggered chain elongation to butanol (1.5-fold) production but did not change the alcohol:acid ratio. Flux balance analysis showed that CO served both as a carbon and energy source, and CO mixotrophy displayed a carbon and energy efficiency of 45 and 77%, respectively. This study expands the knowledge on physiology and metabolism of C.carboxidivorans and can serve as the starting point for rational engineering and process intensification to establish efficient production of alcohols and acids from carbon waste.
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Affiliation(s)
- Charlotte Anne Vees
- Technische Universität Wien, Institute of Chemical, Environmental and Bioscience Engineering, Research Area Biochemical Engineering, Gumpendorfer Straße 1a, 1060 Vienna, Austria.
| | - Christoph Herwig
- Technische Universität Wien, Institute of Chemical, Environmental and Bioscience Engineering, Research Area Biochemical Engineering, Gumpendorfer Straße 1a, 1060 Vienna, Austria; Competence Center CHASE GmbH, Altenbergerstraße 69, 4040 Linz, Austria.
| | - Stefan Pflügl
- Technische Universität Wien, Institute of Chemical, Environmental and Bioscience Engineering, Research Area Biochemical Engineering, Gumpendorfer Straße 1a, 1060 Vienna, Austria.
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11
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Herzog J, Mook A, Guhl L, Bäumler M, Beck MH, Weuster‐Botz D, Bengelsdorf FR, Zeng A. Novel synthetic co-culture of Acetobacterium woodii and Clostridium drakei using CO 2 and in situ generated H 2 for the production of caproic acid via lactic acid. Eng Life Sci 2022; 23:e2100169. [PMID: 36619880 PMCID: PMC9815077 DOI: 10.1002/elsc.202100169] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 04/07/2022] [Accepted: 05/06/2022] [Indexed: 01/11/2023] Open
Abstract
Acetobacterium woodii is known to produce mainly acetate from CO2 and H2, but the production of higher value chemicals is desired for the bioeconomy. Using chain-elongating bacteria, synthetic co-cultures have the potential to produce longer-chained products such as caproic acid. In this study, we present first results for a successful autotrophic co-cultivation of A. woodii mutants and a Clostridium drakei wild-type strain in a stirred-tank bioreactor for the production of caproic acid from CO2 and H2 via the intermediate lactic acid. For autotrophic lactate production, a recombinant A. woodii strain with a deleted Lct-dehydrogenase complex, which is encoded by the lctBCD genes, and an inserted D-lactate dehydrogenase (LdhD) originating from Leuconostoc mesenteroides, was used. Hydrogen for the process was supplied using an All-in-One electrode for in situ water electrolysis. Lactate concentrations as high as 0.5 g L-1 were achieved with the AiO-electrode, whereas 8.1 g L-1 lactate were produced with direct H2 sparging in a stirred-tank bioreactor. Hydrogen limitation was identified in the AiO process. However, with cathode surface area enlargement or numbering-up of the electrode and on-demand hydrogen generation, this process has great potential for a true carbon-negative production of value chemicals from CO2.
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Affiliation(s)
- Jan Herzog
- Institute of Bioprocess and Biosystems EngineeringHamburg University of TechnologyHamburgGermany
| | - Alexander Mook
- Institute of Microbiology and BiotechnologyUlm UniversityUlmGermany
| | - Lotta Guhl
- Institute of Bioprocess and Biosystems EngineeringHamburg University of TechnologyHamburgGermany
| | - Miriam Bäumler
- Department of Energy and Process EngineeringChair of Biochemical EngineeringTechnical University of MunichTUM School of Engineering and DesignGarchingGermany
| | - Matthias H. Beck
- Institute of Microbiology and BiotechnologyUlm UniversityUlmGermany
| | - Dirk Weuster‐Botz
- Department of Energy and Process EngineeringChair of Biochemical EngineeringTechnical University of MunichTUM School of Engineering and DesignGarchingGermany
| | | | - An‐Ping Zeng
- Institute of Bioprocess and Biosystems EngineeringHamburg University of TechnologyHamburgGermany
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12
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Lee H, Bae J, Jin S, Kang S, Cho BK. Engineering Acetogenic Bacteria for Efficient One-Carbon Utilization. Front Microbiol 2022; 13:865168. [PMID: 35615514 PMCID: PMC9124964 DOI: 10.3389/fmicb.2022.865168] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 04/19/2022] [Indexed: 12/03/2022] Open
Abstract
C1 gases, including carbon dioxide (CO2) and carbon monoxide (CO), are major contributors to climate crisis. Numerous studies have been conducted to fix and recycle C1 gases in order to solve this problem. Among them, the use of microorganisms as biocatalysts to convert C1 gases to value-added chemicals is a promising solution. Acetogenic bacteria (acetogens) have received attention as high-potential biocatalysts owing to their conserved Wood–Ljungdahl (WL) pathway, which fixes not only CO2 but also CO. Although some metabolites have been produced via C1 gas fermentation on an industrial scale, the conversion of C1 gases to produce various biochemicals by engineering acetogens has been limited. The energy limitation of acetogens is one of the challenges to overcome, as their metabolism operates at a thermodynamic limit, and the low solubility of gaseous substrates results in a limited supply of cellular energy. This review provides strategies for developing efficient platform strains for C1 gas conversion, focusing on engineering the WL pathway. Supplying liquid C1 substrates, which can be obtained from CO2, or electricity is introduced as a strategy to overcome the energy limitation. Future prospective approaches on engineering acetogens based on systems and synthetic biology approaches are also discussed.
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Affiliation(s)
- Hyeonsik Lee
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Jiyun Bae
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Sangrak Jin
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Seulgi Kang
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Byung-Kwan Cho
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
- KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
- *Correspondence: Byung-Kwan Cho,
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Heffernan JK, Mahamkali V, Valgepea K, Marcellin E, Nielsen LK. Analytical tools for unravelling the metabolism of gas-fermenting Clostridia. Curr Opin Biotechnol 2022; 75:102700. [PMID: 35240422 DOI: 10.1016/j.copbio.2022.102700] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 01/24/2022] [Accepted: 02/05/2022] [Indexed: 12/23/2022]
Abstract
Acetogens harness the Wood-Ljungdahl Pathway, a unique metabolic pathway for C1 capture close to the thermodynamic limit. Gas fermentation using acetogens is already used for CO-to-ethanol conversion at industrial-scale and has the potential to valorise a range of C1 and waste substrates to short-chain and medium-chain carboxylic acids and alcohols. Advances in analytical quantification and metabolic modelling have helped guide industrial gas fermentation designs. Further advances in the measurements of difficult to measure metabolites are required to improve kinetic modelling and understand the regulation of acetogen metabolism. This will help guide future synthetic biology designs needed to realise the full potential of gas fermentation in stimulating a circular bioeconomy.
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Affiliation(s)
- James K Heffernan
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Vishnu Mahamkali
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Kaspar Valgepea
- ERA Chair in Gas Fermentation Technologies, Institute of Technology, University of Tartu, Tartu 50411, Estonia
| | - Esteban Marcellin
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD 4072, Australia; Queensland Node of Metabolomics Australia, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Lars K Nielsen
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD 4072, Australia; Queensland Node of Metabolomics Australia, The University of Queensland, Brisbane, QLD 4072, Australia; The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby DK-2800, Denmark.
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Autotrophic lactate production from H2 + CO2 using recombinant and fluorescent FAST-tagged Acetobacterium woodii strains. Appl Microbiol Biotechnol 2022; 106:1447-1458. [PMID: 35092454 PMCID: PMC8882112 DOI: 10.1007/s00253-022-11770-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 12/23/2021] [Accepted: 01/07/2022] [Indexed: 12/12/2022]
Abstract
AbstractLactate has various uses as industrial platform chemical, poly-lactic acid precursor or feedstock for anaerobic co-cultivations. The aim of this study was to construct and characterise Acetobacterium woodii strains capable of autotrophic lactate production. Therefore, the lctBCD genes, encoding the native Lct dehydrogenase complex, responsible for lactate consumption, were knocked out. Subsequently, a gene encoding a d-lactate dehydrogenase (LDHD) originating from Leuconostoc mesenteroides was expressed in A. woodii, either under the control of the anhydrotetracycline-inducible promoter Ptet or under the lactose-inducible promoter PbgaL. Moreover, LDHD was N-terminally fused to the oxygen-independent fluorescence-activating and absorption-shifting tag (FAST) and expressed in respective A. woodii strains. Cells that produced the LDHD fusion protein were capable of lactate production of up to 18.8 mM in autotrophic batch experiments using H2 + CO2 as energy and carbon source. Furthermore, cells showed a clear and bright fluorescence during exponential growth, as well as in the stationary phase after induction, mediated by the N-terminal FAST. Flow cytometry at the single-cell level revealed phenotypic heterogeneities for cells expressing the FAST-tagged LDHD fusion protein. This study shows that FAST provides a new reporter tool to quickly analyze gene expression over the course of growth experiments of A. woodii. Consequently, fluorescence-based reporters allow for faster and more targeted optimization of production strains.Key points
•Autotrophic lactate production was achieved with A. woodii.
•FAST functions as fluorescent marker protein in A. woodii.
•Fluorescence measurements on single-cell level revealed population heterogeneity.
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