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Golzar-Ahmadi M, Bahaloo-Horeh N, Pourhossein F, Norouzi F, Schoenberger N, Hintersatz C, Chakankar M, Holuszko M, Kaksonen AH. Pathway to industrial application of heterotrophic organisms in critical metals recycling from e-waste. Biotechnol Adv 2024:108438. [PMID: 39218325 DOI: 10.1016/j.biotechadv.2024.108438] [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: 03/26/2024] [Revised: 07/30/2024] [Accepted: 08/27/2024] [Indexed: 09/04/2024]
Abstract
The transition to renewable energies and electric vehicles has triggered an unprecedented demand for metals. Sustainable development of these technologies relies on effectively managing the lifecycle of critical raw materials, including their responsible sourcing, efficient use, and recycling. Metal recycling from electronic waste (e-waste) is of paramount importance owing to ore exceeding amounts of critical elements and high toxicity of heavy metals and organic pollutants in e-waste to the natural ecosystem and human body. Heterotrophic microbes secrete numerous metal-binding biomolecules such as organic acids, amino acids, cyanide, siderophores, peptides, and biosurfactants which can be utilized for eco-friendly and profitable metal recycling. In this review paper, we presented a critical review of heterotrophic organisms in biomining, and current barriers hampering the industrial application of organic acid bioleaching and biocyanide leaching. We also discussed how these challenges can be surmounted with simple methods (e.g., culture media optimization, separation of microbial growth and metal extraction process) and state-of-the-art biological approaches (e.g., artificial microbial community, synthetic biology, metabolic engineering, advanced fermentation strategies, and biofilm engineering). Lastly, we showcased emerging technologies (e.g., artificially synthesized peptides, siderophores, and biosurfactants) derived from heterotrophs with the potential for inexpensive, low-impact, selective and advanced metal recovery from bioleaching solutions.
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Affiliation(s)
- Mehdi Golzar-Ahmadi
- Norman B. Keevil Institute of Mining Engineering, University of British Columbia, Vancouver, Canada
| | | | - Fatemeh Pourhossein
- Research Centre for Health & Life Sciences, Coventry University, Coventry, UK
| | - Forough Norouzi
- Norman B. Keevil Institute of Mining Engineering, University of British Columbia, Vancouver, Canada
| | - Nora Schoenberger
- Helmholtz Institute Freiberg for Resource Technology, Bautzner Landstrasse 400, Dresden, Germany
| | - Christian Hintersatz
- Helmholtz Institute Freiberg for Resource Technology, Bautzner Landstrasse 400, Dresden, Germany
| | - Mital Chakankar
- Helmholtz Institute Freiberg for Resource Technology, Bautzner Landstrasse 400, Dresden, Germany
| | - Maria Holuszko
- Norman B. Keevil Institute of Mining Engineering, University of British Columbia, Vancouver, Canada.
| | - Anna H Kaksonen
- Commonwealth Scientific and Industrial Research Organization (CSIRO) Environment, Western Australia, Australia.
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2
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Bae J, Park C, Jung H, Jin S, Cho BK. Harnessing acetogenic bacteria for one-carbon valorization toward sustainable chemical production. RSC Chem Biol 2024; 5:812-832. [PMID: 39211478 PMCID: PMC11353040 DOI: 10.1039/d4cb00099d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2024] [Accepted: 07/06/2024] [Indexed: 09/04/2024] Open
Abstract
The pressing climate change issues have intensified the need for a rapid transition towards a bio-based circular carbon economy. Harnessing acetogenic bacteria as biocatalysts to convert C1 compounds such as CO2, CO, formate, or methanol into value-added multicarbon chemicals is a promising solution for both carbon capture and utilization, enabling sustainable and green chemical production. Recent advances in the metabolic engineering of acetogens have expanded the range of commodity chemicals and biofuels produced from C1 compounds. However, producing energy-demanding high-value chemicals on an industrial scale from C1 substrates remains challenging because of the inherent energetic limitations of acetogenic bacteria. Therefore, overcoming this hurdle is necessary to scale up the acetogenic C1 conversion process and realize a circular carbon economy. This review overviews the acetogenic bacteria and their potential as sustainable and green chemical production platforms. Recent efforts to address these challenges have focused on enhancing the ATP and redox availability of acetogens to improve their energetics and conversion performances. Furthermore, promising technologies that leverage low-cost, sustainable energy sources such as electricity and light are discussed to improve the sustainability of the overall process. Finally, we review emerging technologies that accelerate the development of high-performance acetogenic bacteria suitable for industrial-scale production and address the economic sustainability of acetogenic C1 conversion. Overall, harnessing acetogenic bacteria for C1 valorization offers a promising route toward sustainable and green chemical production, aligning with the circular economy concept.
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Affiliation(s)
- Jiyun Bae
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology Daejeon 34141 Republic of Korea
| | - Chanho Park
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology Daejeon 34141 Republic of Korea
| | - Hyunwoo Jung
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology Daejeon 34141 Republic of Korea
| | - Sangrak Jin
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology Daejeon 34141 Republic of Korea
| | - Byung-Kwan Cho
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology Daejeon 34141 Republic of Korea
- KAIST Institute for the BioCentury, Korea Advanced Institute of Science and Technology Daejeon 34141 Republic of Korea
- Graduate School of Engineering Biology, Korea Advanced Institute of Science and Technology Daejeon 34141 Republic of Korea
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3
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Sanford P, Woolston BM. Development of a Recombineering System for the Acetogen Eubacterium limosum with Cas9 Counterselection for Markerless Genome Engineering. ACS Synth Biol 2024; 13:2505-2514. [PMID: 39033464 PMCID: PMC11334238 DOI: 10.1021/acssynbio.4c00253] [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: 04/09/2024] [Revised: 07/03/2024] [Accepted: 07/08/2024] [Indexed: 07/23/2024]
Abstract
Eubacterium limosum is a Clostridial acetogen that efficiently utilizes a wide range of single-carbon substrates and contributes to metabolism of health-associated compounds in the human gut microbiota. These traits have led to interest in developing it as a platform for sustainable CO2-based biofuel production to combat carbon emissions, and for exploring the importance of the microbiota in human health. However, synthetic biology and metabolic engineering in E. limosum have been hindered by the inability to rapidly make precise genomic modifications. Here, we screened a diverse library of recombinase proteins to develop a highly efficient oligonucleotide-based recombineering system based on the viral recombinase RecT. Following optimization, the system is capable of catalyzing ssDNA recombination at an efficiency of up to 2%. Addition of a Cas9 counterselection system eliminated unrecombined cells, with up to 100% of viable cells encoding the desired mutation, enabling creation of genomic point mutations in a scarless and markerless manner. We deployed this system to create a clean knockout of the extracellular polymeric substance (EPS) gene cluster, generating a strain incapable of biofilm formation. This approach is rapid and simple, not requiring laborious homology arm cloning, and can readily be retargeted to almost any genomic locus. This work overcomes a major bottleneck in E. limosum genetic engineering by enabling precise genomic modifications, and provides both a roadmap and associated recombinase plasmid library for developing similar systems in other Clostridia of interest.
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Affiliation(s)
- Patrick
A. Sanford
- Department of Chemical Engineering, Northeastern University, 360 Huntington Avenue, 223 Cullinane, Boston, Massachusetts 02115, United States
| | - Benjamin M. Woolston
- Department of Chemical Engineering, Northeastern University, 360 Huntington Avenue, 223 Cullinane, Boston, Massachusetts 02115, United States
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4
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Zhang JZ, Li YZ, Xi ZN, Gao HP, Zhang Q, Liu LC, Li FL, Ma XQ. Engineered acetogenic bacteria as microbial cell factory for diversified biochemicals. Front Bioeng Biotechnol 2024; 12:1395540. [PMID: 39055341 PMCID: PMC11269201 DOI: 10.3389/fbioe.2024.1395540] [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: 03/04/2024] [Accepted: 06/28/2024] [Indexed: 07/27/2024] Open
Abstract
Acetogenic bacteria (acetogens) are a class of microorganisms with conserved Wood-Ljungdahl pathway that can utilize CO and CO2/H2 as carbon source for autotrophic growth and convert these substrates to acetate and ethanol. Acetogens have great potential for the sustainable production of biofuels and bulk biochemicals using C1 gases (CO and CO2) from industrial syngas and waste gases, which play an important role in achieving carbon neutrality. In recent years, with the development and improvement of gene editing methods, the metabolic engineering of acetogens is making rapid progress. With introduction of heterogeneous metabolic pathways, acetogens can improve the production capacity of native products or obtain the ability to synthesize non-native products. This paper reviews the recent application of metabolic engineering in acetogens. In addition, the challenges of metabolic engineering in acetogens are indicated, and strategies to address these challenges are also discussed.
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Affiliation(s)
- Jun-Zhe Zhang
- Qingdao C1 Refinery Engineering Research Center, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yu-Zhen Li
- Qingdao C1 Refinery Engineering Research Center, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zhi-Ning Xi
- Qingdao C1 Refinery Engineering Research Center, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
| | - Hui-Peng Gao
- Sinopec Dalian (Fushun) Research Institute of Petroleum and Petrochemicals, Dalian, China
| | - Quan Zhang
- Sinopec Dalian (Fushun) Research Institute of Petroleum and Petrochemicals, Dalian, China
| | - Li-Cheng Liu
- Key Laboratory of Marine Chemistry Theory and Technology (Ministry of Education), College of Chemistry and Chemical Engineering, Ocean University of China, Qingdao, China
| | - Fu-Li Li
- Qingdao C1 Refinery Engineering Research Center, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
- Shandong Energy Institute, Qingdao, China
- Qingdao New Energy Shandong Laboratory, Qingdao, China
| | - Xiao-Qing Ma
- Qingdao C1 Refinery Engineering Research Center, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
- Qingdao New Energy Shandong Laboratory, Qingdao, China
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5
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De Marchi D, Shaposhnikov R, Gobaa S, Pastorelli D, Batt G, Magni P, Pasotti L. Design and Model-Driven Analysis of Synthetic Circuits with the Staphylococcus aureus Dead-Cas9 (sadCas9) as a Programmable Transcriptional Regulator in Bacteria. ACS Synth Biol 2024; 13:763-780. [PMID: 38374729 DOI: 10.1021/acssynbio.3c00541] [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] [Indexed: 02/21/2024]
Abstract
Synthetic circuit design is crucial for engineering microbes that process environmental cues and provide biologically relevant outputs. To reliably scale-up circuit complexity, the availability of parts toolkits is central. Streptococcus pyogenes (sp)-derived CRISPR interference/dead-Cas9 (CRISPRi/spdCas9) is widely adopted for implementing programmable regulations in synthetic circuits, and alternative CRISPRi systems will further expand our toolkits of orthogonal components. Here, we showcase the potential of CRISPRi using the engineered dCas9 from Staphylococcus aureus (sadCas9), not previously used in bacterial circuits, that is attractive for its low size and high specificity. We designed a collection of ∼20 increasingly complex circuits and variants in Escherichia coli, including circuits with static function like one-/two-input logic gates (NOT, NAND), circuits with dynamic behavior like incoherent feedforward loops (iFFLs), and applied sadCas9 to fix a T7 polymerase-based cascade. Data demonstrated specific and efficient target repression (100-fold) and qualitatively successful functioning for all circuits. Other advantageous features included low sadCas9-borne cell load and orthogonality with spdCas9. However, different circuit variants showed quantitatively unexpected and previously unreported steady-state responses: the dynamic range, switch point, and slope of NOT/NAND gates changed for different output promoters, and a multiphasic behavior was observed in iFFLs, differing from the expected bell-shaped or sigmoidal curves. Model analysis explained the observed curves by complex interplays among components, due to reporter gene-borne cell load and regulator competition. Overall, CRISPRi/sadCas9 successfully expanded the available toolkit for bacterial engineering. Analysis of our circuit collection depicted the impact of generally neglected effects modulating the shape of component dose-response curves, to avoid drawing wrong conclusions on circuit functioning.
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Affiliation(s)
- Davide De Marchi
- Department of Electrical, Computer and Biomedical Engineering, University of Pavia, via Ferrata 5, 27100 Pavia, Italy
- Centre for Health Technologies, University of Pavia, via Ferrata 5, 27100 Pavia, Italy
| | - Roman Shaposhnikov
- Department of Electrical, Computer and Biomedical Engineering, University of Pavia, via Ferrata 5, 27100 Pavia, Italy
- Centre for Health Technologies, University of Pavia, via Ferrata 5, 27100 Pavia, Italy
| | - Samy Gobaa
- Institut Pasteur, Université Paris Cité, Biomaterials and Microfluidics Core Facility, 28 Rue du Docteur Roux, 75015 Paris, France
| | - Daniele Pastorelli
- Department of Electrical, Computer and Biomedical Engineering, University of Pavia, via Ferrata 5, 27100 Pavia, Italy
- Centre for Health Technologies, University of Pavia, via Ferrata 5, 27100 Pavia, Italy
| | - Gregory Batt
- Institut Pasteur, Inria, Université Paris Cité, 28 rue du Docteur Roux, 75015 Paris, France
| | - Paolo Magni
- Department of Electrical, Computer and Biomedical Engineering, University of Pavia, via Ferrata 5, 27100 Pavia, Italy
- Centre for Health Technologies, University of Pavia, via Ferrata 5, 27100 Pavia, Italy
| | - Lorenzo Pasotti
- Department of Electrical, Computer and Biomedical Engineering, University of Pavia, via Ferrata 5, 27100 Pavia, Italy
- Centre for Health Technologies, University of Pavia, via Ferrata 5, 27100 Pavia, Italy
- Institut Pasteur, Inria, Université Paris Cité, 28 rue du Docteur Roux, 75015 Paris, France
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6
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Flaiz M, Poehlein A, Wilhelm W, Mook A, Daniel R, Dürre P, Bengelsdorf FR. Refining and illuminating acetogenic Eubacterium strains for reclassification and metabolic engineering. Microb Cell Fact 2024; 23:24. [PMID: 38233843 PMCID: PMC10795377 DOI: 10.1186/s12934-024-02301-8] [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: 10/27/2023] [Accepted: 01/09/2024] [Indexed: 01/19/2024] Open
Abstract
BACKGROUND The genus Eubacterium is quite diverse and includes several acetogenic strains capable of fermenting C1-substrates into valuable products. Especially, Eubacterium limosum and closely related strains attract attention not only for their capability to ferment C1 gases and liquids, but also due to their ability to produce butyrate. Apart from its well-elucidated metabolism, E. limosum is also genetically accessible, which makes it an interesting candidate to be an industrial biocatalyst. RESULTS In this study, we examined genomic, phylogenetic, and physiologic features of E. limosum and the closest related species E. callanderi as well as E. maltosivorans. We sequenced the genomes of the six Eubacterium strains 'FD' (DSM 3662T), 'Marburg' (DSM 3468), '2A' (DSM 2593), '11A' (DSM 2594), 'G14' (DSM 107592), and '32' (DSM 20517) and subsequently compared these with previously available genomes of the E. limosum type strain (DSM 20543T) as well as the strains 'B2', 'KIST612', 'YI' (DSM 105863T), and 'SA11'. This comparison revealed a close relationship between all eleven Eubacterium strains, forming three distinct clades: E. limosum, E. callanderi, and E. maltosivorans. Moreover, we identified the gene clusters responsible for methanol utilization as well as genes mediating chain elongation in all analyzed strains. Subsequent growth experiments revealed that strains of all three clades can convert methanol and produce acetate, butyrate, and hexanoate via reverse β-oxidation. Additionally, we used a harmonized electroporation protocol and successfully transformed eight of these Eubacterium strains to enable recombinant plasmid-based expression of the gene encoding the fluorescence-activating and absorption shifting tag (FAST). Engineered Eubacterium strains were verified regarding their FAST-mediated fluorescence at a single-cell level using a flow cytometry approach. Eventually, strains 'FD' (DSM 3662T), '2A' (DSM 2593), '11A' (DSM 2594), and '32' (DSM 20517) were genetically engineered for the first time. CONCLUSION Strains of E. limosum, E. callanderi, and E. maltosivorans are outstanding candidates as biocatalysts for anaerobic C1-substrate conversion into valuable biocommodities. A large variety of strains is genetically accessible using a harmonized electroporation protocol, and FAST can serve as a reliable fluorescent reporter protein to characterize genetically engineered cells. In total eleven strains have been assigned to distinct clades, providing a clear and updated classification. Thus, the description of respective Eubacterium species has been emended, improved, aligned, and is requested to be implemented in respective databases.
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Affiliation(s)
- Maximilian Flaiz
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, The Netherlands.
- Institute of Microbiology and Biotechnology, University of Ulm, Ulm, Germany.
| | - Anja Poehlein
- Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Georg-August University, Göttingen, Germany
| | - Wiebke Wilhelm
- Institute of Microbiology and Biotechnology, University of Ulm, Ulm, Germany
| | - Alexander Mook
- Institute of Molecular Biology and Biotechnology of Prokaryotes, University of Ulm, Ulm, Germany
| | - Rolf Daniel
- Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Georg-August University, Göttingen, Germany
| | - Peter Dürre
- Institute of Microbiology and Biotechnology, University of Ulm, Ulm, Germany
| | - Frank R Bengelsdorf
- Institute of Molecular Biology and Biotechnology of Prokaryotes, University of Ulm, Ulm, Germany.
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7
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François JM. Progress advances in the production of bio-sourced methionine and its hydroxyl analogues. Biotechnol Adv 2023; 69:108259. [PMID: 37734648 DOI: 10.1016/j.biotechadv.2023.108259] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 08/11/2023] [Accepted: 09/15/2023] [Indexed: 09/23/2023]
Abstract
The essential sulphur-containing amino acid, methionine, is becoming a mass-commodity product with an annual production that exceeded 1,500,000 tons in 2018. This amino acid is today almost exclusively produced by chemical process from fossil resources. The environmental problems caused by this industrial process, and the expected scarcity of oil resources in the coming years, have recently accelerated the development of bioprocesses for producing methionine from renewable carbon feedstock. After a brief description of the chemical process and the techno-economic context that still justify the production of methionine by petrochemical processes, this review will present the current state of the art of biobased alternatives aiming at a sustainable production of this amino acid and its hydroxyl analogues from renewable carbon feedstock. In particular, this review will focus on three bio-based processes, namely a purely fermentative process based on the metabolic engineering of the natural methionine pathway, a mixed process combining the production of the O-acetyl/O-succinyl homoserine intermediate of this pathway by fermentation followed by an enzyme-based conversion of this intermediate into L-methionine and lately, a hybrid process in which the non-natural chemical synthon, 2,4-dihydroxybutyric acid, obtained by fermentation of sugars is converted by chemo-catalysis into hydroxyl methionine analogues. The industrial potential of these three bioprocesses, as well as the major technical and economic obstacles that remain to be overcome to reach industrial maturity are discussed. This review concludes by bringing up the assets of these bioprocesses to meet the challenge of the "green transition", with the accomplishment of the objective "zero carbon" by 2050 and how they can be part of a model of Bioeconomy enhancing local resources.
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Affiliation(s)
- Jean Marie François
- Toulouse Biotechnology Institute, UMR INSA -CNRS5504 and UMR INSA-INRAE 792, 135 avenue de Rangueil, 31077 Toulouse, France; Toulouse White Biotechnology, UMS INRAE-INSA-CNRS, 135 Avenue de Rangueil, 31077 Toulouse, France.
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8
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Aminian-Dehkordi J, Rahimi S, Golzar-Ahmadi M, Singh A, Lopez J, Ledesma-Amaro R, Mijakovic I. Synthetic biology tools for environmental protection. Biotechnol Adv 2023; 68:108239. [PMID: 37619824 DOI: 10.1016/j.biotechadv.2023.108239] [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: 04/15/2023] [Revised: 08/17/2023] [Accepted: 08/20/2023] [Indexed: 08/26/2023]
Abstract
Synthetic biology transforms the way we perceive biological systems. Emerging technologies in this field affect many disciplines of science and engineering. Traditionally, synthetic biology approaches were commonly aimed at developing cost-effective microbial cell factories to produce chemicals from renewable sources. Based on this, the immediate beneficial impact of synthetic biology on the environment came from reducing our oil dependency. However, synthetic biology is starting to play a more direct role in environmental protection. Toxic chemicals released by industries and agriculture endanger the environment, disrupting ecosystem balance and biodiversity loss. This review highlights synthetic biology approaches that can help environmental protection by providing remediation systems capable of sensing and responding to specific pollutants. Remediation strategies based on genetically engineered microbes and plants are discussed. Further, an overview of computational approaches that facilitate the design and application of synthetic biology tools in environmental protection is presented.
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Affiliation(s)
| | - Shadi Rahimi
- Department of Life Sciences, Chalmers University of Technology, Göteborg, Sweden
| | - Mehdi Golzar-Ahmadi
- Norman B. Keevil Institute of Mining Engineering, University of British Columbia, Vancouver, Canada
| | - Amritpal Singh
- Department of Bioengineering, Imperial College London, London, SW72AZ, UK
| | - Javiera Lopez
- Department of Bioengineering, Imperial College London, London, SW72AZ, UK
| | | | - Ivan Mijakovic
- Department of Life Sciences, Chalmers University of Technology, Göteborg, Sweden; Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark.
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9
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Fuchs W, Rachbauer L, Rittmann SKMR, Bochmann G, Ribitsch D, Steger F. Eight Up-Coming Biotech Tools to Combat Climate Crisis. Microorganisms 2023; 11:1514. [PMID: 37375016 DOI: 10.3390/microorganisms11061514] [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: 05/19/2023] [Revised: 06/02/2023] [Accepted: 06/05/2023] [Indexed: 06/29/2023] Open
Abstract
Biotechnology has a high potential to substantially contribute to a low-carbon society. Several green processes are already well established, utilizing the unique capacity of living cells or their instruments. Beyond that, the authors believe that there are new biotechnological procedures in the pipeline which have the momentum to add to this ongoing change in our economy. Eight promising biotechnology tools were selected by the authors as potentially impactful game changers: (i) the Wood-Ljungdahl pathway, (ii) carbonic anhydrase, (iii) cutinase, (iv) methanogens, (v) electro-microbiology, (vi) hydrogenase, (vii) cellulosome and, (viii) nitrogenase. Some of them are fairly new and are explored predominantly in science labs. Others have been around for decades, however, with new scientific groundwork that may rigorously expand their roles. In the current paper, the authors summarize the latest state of research on these eight selected tools and the status of their practical implementation. We bring forward our arguments on why we consider these processes real game changers.
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Affiliation(s)
- Werner Fuchs
- Department IFA-Tulln, Institute of Environmental Biotechnology, University of Natural Resources and Life Sciences, Vienna, Konrad-Lorenz-Strasse 20, 3430 Tulln, Austria
| | - Lydia Rachbauer
- Lawrence Berkeley National Laboratory, Deconstruction Division at the Joint Bioenergy Institute, 5885 Hollis Street, Emeryville, CA 94608, USA
| | - Simon K-M R Rittmann
- Archaea Physiology & Biotechnology Group, Department of Functional and Evolutionary Ecology, Universität Wien, Djerassiplatz 1, 1030 Wien, Austria
| | - Günther Bochmann
- Department IFA-Tulln, Institute of Environmental Biotechnology, University of Natural Resources and Life Sciences, Vienna, Konrad-Lorenz-Strasse 20, 3430 Tulln, Austria
| | - Doris Ribitsch
- ACIB-Austrian Centre of Industrial Biotechnology, Krenngasse 37, 8010 Graz, Austria
| | - Franziska Steger
- Department IFA-Tulln, Institute of Environmental Biotechnology, University of Natural Resources and Life Sciences, Vienna, Konrad-Lorenz-Strasse 20, 3430 Tulln, Austria
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10
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Nwaokorie UJ, Reinmets K, de Lima LA, Pawar PR, Shaikh KM, Harris A, Köpke M, Valgepea K. Deletion of genes linked to the C 1-fixing gene cluster affects growth, by-products, and proteome of Clostridium autoethanogenum. Front Bioeng Biotechnol 2023; 11:1167892. [PMID: 37265994 PMCID: PMC10230548 DOI: 10.3389/fbioe.2023.1167892] [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: 02/16/2023] [Accepted: 05/03/2023] [Indexed: 06/03/2023] Open
Abstract
Gas fermentation has emerged as a sustainable route to produce fuels and chemicals by recycling inexpensive one-carbon (C1) feedstocks from gaseous and solid waste using gas-fermenting microbes. Currently, acetogens that utilise the Wood-Ljungdahl pathway to convert carbon oxides (CO and CO2) into valuable products are the most advanced biocatalysts for gas fermentation. However, our understanding of the functionalities of the genes involved in the C1-fixing gene cluster and its closely-linked genes is incomplete. Here, we investigate the role of two genes with unclear functions-hypothetical protein (hp; LABRINI_07945) and CooT nickel binding protein (nbp; LABRINI_07950)-directly adjacent and expressed at similar levels to the C1-fixing gene cluster in the gas-fermenting model-acetogen Clostridium autoethanogenum. Targeted deletion of either the hp or nbp gene using CRISPR/nCas9, and phenotypic characterisation in heterotrophic and autotrophic batch and autotrophic bioreactor continuous cultures revealed significant growth defects and altered by-product profiles for both ∆hp and ∆nbp strains. Variable effects of gene deletion on autotrophic batch growth on rich or minimal media suggest that both genes affect the utilisation of complex nutrients. Autotrophic chemostat cultures showed lower acetate and ethanol production rates and higher carbon flux to CO2 and biomass for both deletion strains. Additionally, proteome analysis revealed that disruption of either gene affects the expression of proteins of the C1-fixing gene cluster and ethanol synthesis pathways. Our work contributes to a better understanding of genotype-phenotype relationships in acetogens and offers engineering targets to improve carbon fixation efficiency in gas fermentation.
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Affiliation(s)
- Ugochi Jennifer Nwaokorie
- ERA Chair in Gas Fermentation Technologies, Institute of Technology, University of Tartu, Tartu, Estonia
| | - Kristina Reinmets
- ERA Chair in Gas Fermentation Technologies, Institute of Technology, University of Tartu, Tartu, Estonia
| | - Lorena Azevedo de Lima
- ERA Chair in Gas Fermentation Technologies, Institute of Technology, University of Tartu, Tartu, Estonia
| | - Pratik Rajendra Pawar
- ERA Chair in Gas Fermentation Technologies, Institute of Technology, University of Tartu, Tartu, Estonia
| | | | | | | | - Kaspar Valgepea
- ERA Chair in Gas Fermentation Technologies, Institute of Technology, University of Tartu, Tartu, Estonia
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11
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Moreira JPC, Heap JT, Alves JI, Domingues L. Developing a genetic engineering method for Acetobacterium wieringae to expand one-carbon valorization pathways. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2023; 16:24. [PMID: 36788587 PMCID: PMC9930230 DOI: 10.1186/s13068-023-02259-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 01/05/2023] [Indexed: 02/16/2023]
Abstract
BACKGROUND Developing new bioprocesses to produce chemicals and fuels with reduced production costs will greatly facilitate the replacement of fossil-based raw materials. In most fermentation bioprocesses, the feedstock usually represents the highest cost, which becomes the target for cost reduction. Additionally, the biorefinery concept advocates revenue growth from the production of several compounds using the same feedstock. Taken together, the production of bio commodities from low-cost gas streams containing CO, CO2, and H2, obtained from the gasification of any carbon-containing waste streams or off-gases from heavy industry (steel mills, processing plants, or refineries), embodies an opportunity for affordable and renewable chemical production. To achieve this, by studying non-model autotrophic acetogens, current limitations concerning low growth rates, toxicity by gas streams, and low productivity may be overcome. The Acetobacterium wieringae strain JM is a novel autotrophic acetogen that is capable of producing acetate and ethanol. It exhibits faster growth rates on various gaseous compounds, including carbon monoxide, compared to other Acetobacterium species, making it potentially useful for industrial applications. The species A. wieringae has not been genetically modified, therefore developing a genetic engineering method is important for expanding its product portfolio from gas fermentation and overall improving the characteristics of this acetogen for industrial demands. RESULTS This work reports the development and optimization of an electrotransformation protocol for A. wieringae strain JM, which can also be used in A. wieringae DSM 1911, and A. woodii DSM 1030. We also show the functionality of the thiamphenicol resistance marker, catP, and the functionality of the origins of replication pBP1, pCB102, pCD6, and pIM13 in all tested Acetobacterium strains, with transformation efficiencies of up to 2.0 × 103 CFU/μgDNA. Key factors affecting electrotransformation efficiency include OD600 of cell harvesting, pH of resuspension buffer, the field strength of the electric pulse, and plasmid amount. Using this method, the acetone production operon from Clostridium acetobutylicum was efficiently introduced in all tested Acetobacterium spp., leading to non-native biochemical acetone production via plasmid-based expression. CONCLUSIONS A. wieringae can be electrotransformed at high efficiency using different plasmids with different replication origins. The electrotransformation procedure and tools reported here unlock the genetic and metabolic manipulation of the biotechnologically relevant A. wieringae strains. For the first time, non-native acetone production is shown in A. wieringae.
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Affiliation(s)
- João P. C. Moreira
- grid.10328.380000 0001 2159 175XCEB - Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal ,LABBELS - Associate Laboratory, Braga/Guimarães, Portugal
| | - John T. Heap
- grid.4563.40000 0004 1936 8868School of Life Sciences, University of Nottingham, Biodiscovery Institute, University Park, Nottingham, NG7 2RD UK
| | - Joana I. Alves
- grid.10328.380000 0001 2159 175XCEB - Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal ,LABBELS - Associate Laboratory, Braga/Guimarães, Portugal
| | - Lucília Domingues
- CEB - Centre of Biological Engineering, University of Minho, 4710-057, Braga, Portugal. .,LABBELS - Associate Laboratory, Braga/Guimarães, Portugal.
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12
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Genome-wide CRISPRi screen identifies enhanced autolithotrophic phenotypes in acetogenic bacterium Eubacterium limosum. Proc Natl Acad Sci U S A 2023; 120:e2216244120. [PMID: 36716373 PMCID: PMC9963998 DOI: 10.1073/pnas.2216244120] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Acetogenic bacteria are a unique biocatalyst that highly promises to develop the sustainable bioconversion of carbon oxides (e.g., CO and CO2) into multicarbon biochemicals. Genotype-phenotype relationships are important for engineering their metabolic capability to enhance their biocatalytic performance; however, systemic investigation on the fitness contribution of individual gene has been limited. Here, we report genome-scale CRISPR interference screening using 41,939 guide RNAs designed from the E. limosum genome, one of the model acetogenic species, where all genes were targeted for transcriptional suppression. We investigated the fitness contributions of 96% of the total genes identified, revealing the gene fitness and essentiality for heterotrophic and autotrophic metabolisms. Our data show that the Wood-Ljungdahl pathway, membrane regeneration, membrane protein biosynthesis, and butyrate synthesis are essential for autotrophic acetogenesis in E. limosum. Furthermore, we discovered genes that are repression targets that unbiasedly increased autotrophic growth rates fourfold and acetoin production 1.5-fold compared to the wild-type strain under CO2-H2 conditions. These results provide insight for understanding acetogenic metabolism and genome engineering in acetogenic bacteria.
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13
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Sanford PA, Woolston BM. Expanding the genetic engineering toolbox for the metabolically flexible acetogen Eubacterium limosum. J Ind Microbiol Biotechnol 2022; 49:6650221. [PMID: 35881468 PMCID: PMC9559302 DOI: 10.1093/jimb/kuac019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 06/30/2022] [Indexed: 11/14/2022]
Abstract
Acetogenic bacteria are an increasingly popular choice for producing fuels and chemicals from single carbon (C1) substrates. Eubacterium limosum is a promising acetogen with several native advantages, including the ability to catabolize a wide repertoire of C1 feedstocks and the ability to grow well on agar plates. However, despite its promise as a strain for synthetic biology and metabolic engineering, there are insufficient engineering tools and molecular biology knowledge to leverage its native strengths for these applications. To capitalize on the natural advantages of this organism, here we extended its limited engineering toolbox. We evaluated the copy number of three common plasmid origins of replication and devised a method of controlling copy number and heterologous gene expression level by modulating antibiotic concentration. We further quantitatively assessed the strength and regulatory tightness of a panel of promoters, developing a series of well-characterized vectors for gene expression at varying levels. In addition, we developed a black/white colorimetric genetic reporter assay and leveraged the high oxygen tolerance of E. limosum to develop a simple and rapid transformation protocol that enables benchtop transformation. Finally, we developed two new antibiotic selection markers—doubling the number available for this organism. These developments will enable enhanced metabolic engineering and synthetic biology work with E. limosum.
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Affiliation(s)
- Patrick A Sanford
- Department of Chemical Engineering, Northeastern University, 360 Huntington Avenue, 223 Cullinane, Boston, MA 02115, USA
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14
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Kobayashi S, Kato J, Wada K, Takemura K, Kato S, Fujii T, Iwasaki Y, Aoi Y, Morita T, Matsushika A, Murakami K, Nakashimada Y. Reversible Hydrogenase Activity Confers Flexibility to Balance Intracellular Redox in Moorella thermoacetica. Front Microbiol 2022; 13:897066. [PMID: 35633713 PMCID: PMC9133594 DOI: 10.3389/fmicb.2022.897066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 04/19/2022] [Indexed: 11/13/2022] Open
Abstract
Hydrogen (H2) converted to reducing equivalents is used by acetogens to fix and metabolize carbon dioxide (CO2) to acetate. The utilization of H2 enables not only autotrophic growth, but also mixotrophic metabolism in acetogens, enhancing carbon utilization. This feature seems useful, especially when the carbon utilization efficiency of organic carbon sources is lowered by metabolic engineering to produce reduced chemicals, such as ethanol. The potential advantage was tested using engineered strains of Moorella thermoacetica that produce ethanol. By adding H2 to the fructose-supplied culture, the engineered strains produced increased levels of acetate, and a slight increase in ethanol was observed. The utilization of a knockout strain of the major acetate production pathway, aimed at increasing the carbon flux to ethanol, was unexpectedly hindered by H2-mediated growth inhibition in a dose-dependent manner. Metabolomic analysis showed a significant increase in intracellular NADH levels due to H2 in the ethanol-producing strain. Higher NADH level was shown to be the cause of growth inhibition because the decrease in NADH level by dimethyl sulfoxide (DMSO) reduction recovered the growth. When H2 was not supplemented, the intracellular NADH level was balanced by the reversible electron transfer from NADH oxidation to H2 production in the ethanol-producing strain. Therefore, reversible hydrogenase activity confers the ability and flexibility to balance the intracellular redox state of M. thermoacetica. Tuning of the redox balance is required in order to benefit from H2-supplemented mixotrophy, which was confirmed by engineering to produce acetone.
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Affiliation(s)
- Shunsuke Kobayashi
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashihiroshima, Japan
| | - Junya Kato
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashihiroshima, Japan
| | - Keisuke Wada
- National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
| | - Kaisei Takemura
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashihiroshima, Japan
| | - Setsu Kato
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashihiroshima, Japan
| | - Tatsuya Fujii
- National Institute of Advanced Industrial Science and Technology (AIST), Higashihiroshima, Japan
| | - Yuki Iwasaki
- National Institute of Advanced Industrial Science and Technology (AIST), Higashihiroshima, Japan
| | - Yoshiteru Aoi
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashihiroshima, Japan
| | - Tomotake Morita
- National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
| | - Akinori Matsushika
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashihiroshima, Japan
- National Institute of Advanced Industrial Science and Technology (AIST), Higashihiroshima, Japan
| | - Katsuji Murakami
- National Institute of Advanced Industrial Science and Technology (AIST), Higashihiroshima, Japan
| | - Yutaka Nakashimada
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashihiroshima, Japan
- *Correspondence: Yutaka Nakashimada,
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15
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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: 17] [Impact Index Per Article: 8.5] [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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16
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Recycling carbon for sustainable protein production using gas fermentation. Curr Opin Biotechnol 2022; 76:102723. [PMID: 35487158 DOI: 10.1016/j.copbio.2022.102723] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 02/23/2022] [Accepted: 03/17/2022] [Indexed: 02/07/2023]
Abstract
Current food production practices contribute significantly to climate change. To transition into a sustainable future, a combination of new food habits and a radical food production innovation must occur. Single-cell protein from microbial fermentation can profoundly impact sustainability. This review paper explores opportunities offered by gas fermentation to completely replace our reliance on fossil fuels for the production of food. Together with synthetic biology, designed microbial proteins from gas fermentation have the potential to reduce our dependence on fossil fuels and make food production more sustainable.
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17
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Development of highly characterized genetic bioparts for efficient gene expression in CO2-fixing Eubacterium limosum. Metab Eng 2022; 72:215-226. [DOI: 10.1016/j.ymben.2022.03.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 03/20/2022] [Accepted: 03/26/2022] [Indexed: 12/22/2022]
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18
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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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19
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Carbon-negative production of acetone and isopropanol by gas fermentation at industrial pilot scale. Nat Biotechnol 2022; 40:335-344. [DOI: 10.1038/s41587-021-01195-w] [Citation(s) in RCA: 45] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 12/09/2021] [Indexed: 12/21/2022]
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20
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Flaiz M, Baur T, Gaibler J, Kröly C, Dürre P. Establishment of Green- and Red-Fluorescent Reporter Proteins Based on the Fluorescence-Activating and Absorption-Shifting Tag for Use in Acetogenic and Solventogenic Anaerobes. ACS Synth Biol 2022; 11:953-967. [PMID: 35081709 DOI: 10.1021/acssynbio.1c00554] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Anaerobic bacteria are promising biocatalysts to produce industrially relevant products from nonfood feedstocks. Several anaerobes are genetically accessible, and various molecular tools for metabolic engineering are available. Still, the use of bright fluorescent reporters, which are commonly used in molecular biological approaches is limited under anaerobic conditions. Therefore, the establishment of different anaerobic fluorescent reporter proteins is of great interest. Here, we present the establishment of the green- and red-fluorescent reporter proteins greenFAST and redFAST for use in different solventogenic and acetogenic bacteria. Green fluorescence of greenFAST was bright in Clostridium saccharoperbutylacetonicum, Clostridium acetobutylicum, Acetobacterium woodii, and Eubacterium limosum, while only C. saccharoperbutylacetonicum showed bright red fluorescence when producing redFAST. We used both reporter proteins in C. saccharoperbutylacetonicum for multicolor approaches. These include the investigation of the co-culture dynamics of metabolically engineered strains. Moreover, we established a tightly regulated inducible two-plasmid system and used greenFAST and redFAST to track the coexistence and interaction of both plasmids under anaerobic conditions in C. saccharoperbutylacetonicum. The establishment of greenFAST and redFAST as fluorescent reporters opens the door for further multicolor approaches to investigate cell dynamics, gene expression, or protein localization under anaerobic conditions.
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Affiliation(s)
- Maximilian Flaiz
- Institute of Microbiology and Biotechnology, University of Ulm, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Tina Baur
- Institute of Microbiology and Biotechnology, University of Ulm, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Jana Gaibler
- Institute of Microbiology and Biotechnology, University of Ulm, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Christian Kröly
- Institute of Microbiology and Biotechnology, University of Ulm, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Peter Dürre
- Institute of Microbiology and Biotechnology, University of Ulm, Albert-Einstein-Allee 11, 89081 Ulm, Germany
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21
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Establishing Butyribacterium methylotrophicum as a platform organism for the production of biocommodities from liquid C1 metabolites. Appl Environ Microbiol 2022; 88:e0239321. [PMID: 35138930 DOI: 10.1128/aem.02393-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Using the Wood-Ljungdahl pathway, acetogens can non-photosynthetically fix gaseous C1 molecules preventing them from entering the atmosphere. Many acetogens can also grow on liquid C1 compounds such as formate and methanol which avoid the storage and mass transfer issues associated with gaseous C1 compounds. Substrate redox state also plays an important role in acetogen metabolism and can modulate products formed by these organisms. Butyribacterium methylotrophicum is an acetogen known for its ability to synthesize longer-chained molecules such as butyrate and butanol, which have significantly higher value than acetate or ethanol, from one-carbon (C1) compounds. We explored B. methylotrophicum's C1 metabolism by varying substrates, substrate concentrations and substrate feeding strategies to improve four-carbon product titers. Our results showed that formate utilization by B. methylotrophicum favored acetate production and methanol utilization favored butyrate production. Co-feeding of both substrates produced a high butyrate titer of 4 g/L when methanol was supplied in excess to formate. Testing of formate feeding strategies, in the presence of methanol, led to further increases in the butyrate to acetate ratio. Mixotrophic growth of liquid and gaseous C1 substrates expanded the B. methylotrophicum product profile as ethanol, butanol and lactate were produced in these conditions. We also showed that B. methylotrophicum is capable of producing caproate, a six-carbon product, presumably through chain elongation cycles of the reverse β-oxidation pathway. Furthermore, we demonstrated butanol production via heterologous gene expression. Our results indicate that both selection of appropriate substrates and genetic engineering play important roles in determining titers of desired products. Importance. Acetogenic bacteria can fix single-carbon (C1) molecules. However, improvements are needed to overcome poor product titers. Butyribacterium methylotrophicum can naturally ferment C1 compounds into longer-chained molecules such as butyrate alongside traditional acetate. Here we show that B. methylotrophicum can effectively grow on formate and methanol to produce high titers of butyrate. We improved ratios of butyrate to acetate through adjusted formate feeding strategies and produced higher value six-carbon molecules. We also expanded the B. methylotrophicum product profile with the addition of C1 gases as the organism produced ethanol, butanol and lactate. Furthermore, we developed a transformation protocol for B. methylotrophicum to facilitate genetic engineering of this organism for the circular bioeconomy.
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Piatek P, Humphreys C, Raut MP, Wright PC, Simpson S, Köpke M, Minton NP, Winzer K. Agr Quorum Sensing influences the Wood-Ljungdahl pathway in Clostridium autoethanogenum. Sci Rep 2022; 12:411. [PMID: 35013405 PMCID: PMC8748961 DOI: 10.1038/s41598-021-03999-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 12/07/2021] [Indexed: 01/04/2023] Open
Abstract
Acetogenic bacteria are capable of fermenting CO2 and carbon monoxide containing waste-gases into a range of platform chemicals and fuels. Despite major advances in genetic engineering and improving these biocatalysts, several important physiological functions remain elusive. Among these is quorum sensing, a bacterial communication mechanism known to coordinate gene expression in response to cell population density. Two putative agr systems have been identified in the genome of Clostridium autoethanogenum suggesting bacterial communication via autoinducing signal molecules. Signal molecule-encoding agrD1 and agrD2 genes were targeted for in-frame deletion. During heterotrophic growth on fructose as a carbon and energy source, single deletions of either gene did not produce an observable phenotype. However, when both genes were simultaneously inactivated, final product concentrations in the double mutant shifted to a 1.5:1 ratio of ethanol:acetate, compared to a 0.2:1 ratio observed in the wild type control, making ethanol the dominant fermentation product. Moreover, CO2 re-assimilation was also notably reduced in both hetero- and autotrophic growth conditions. These findings were supported through comparative proteomics, which showed lower expression of carbon monoxide dehydrogenase, formate dehydrogenase A and hydrogenases in the ∆agrD1∆agrD2 double mutant, but higher levels of putative alcohol and aldehyde dehydrogenases and bacterial micro-compartment proteins. These findings suggest that Agr quorum sensing, and by inference, cell density play a role in carbon resource management and use of the Wood-Ljungdahl pathway as an electron sink.
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Affiliation(s)
- Pawel Piatek
- Department of Biotechnology and Nanomedicine, SINTEF Industry, 7465, Trondheim, Norway
- BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), School of Life Sciences, University Park, The University of Nottingham, Nottingham, UK
| | - Christopher Humphreys
- BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), School of Life Sciences, University Park, The University of Nottingham, Nottingham, UK
| | - Mahendra P Raut
- Department of Chemical and Biological Engineering, The ChELSI Institute, University of Sheffield, Mappin Street, Sheffield, S1 3JD, UK
| | - Phillip C Wright
- University of Southampton, University Road, Southampton, SO17 1BJ, UK
| | - Sean Simpson
- LanzaTech Inc., 8045 Lamon Ave, Suite 400, Skokie, IL, 60077, USA
| | - Michael Köpke
- LanzaTech Inc., 8045 Lamon Ave, Suite 400, Skokie, IL, 60077, USA
| | - Nigel P Minton
- BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), School of Life Sciences, University Park, The University of Nottingham, Nottingham, UK
| | - Klaus Winzer
- BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), School of Life Sciences, University Park, The University of Nottingham, Nottingham, UK.
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23
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Pavan M, Reinmets K, Garg S, Mueller AP, Marcellin E, Köpke M, Valgepea K. Advances in systems metabolic engineering of autotrophic carbon oxide-fixing biocatalysts towards a circular economy. Metab Eng 2022; 71:117-141. [DOI: 10.1016/j.ymben.2022.01.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 01/24/2022] [Accepted: 01/25/2022] [Indexed: 12/16/2022]
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24
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Hong Y, Zeng AP. Biosynthesis Based on One-Carbon Mixotrophy. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2022; 180:351-371. [DOI: 10.1007/10_2021_198] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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25
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Lee J. Lessons from Clostridial Genetics: Toward Engineering Acetogenic Bacteria. BIOTECHNOL BIOPROC E 2021. [DOI: 10.1007/s12257-021-0062-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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26
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Sanford PA, Woolston BM. Synthetic or natural? Metabolic engineering for assimilation and valorization of methanol. Curr Opin Biotechnol 2021; 74:171-179. [PMID: 34952430 DOI: 10.1016/j.copbio.2021.12.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Revised: 11/23/2021] [Accepted: 12/01/2021] [Indexed: 01/01/2023]
Abstract
Single carbon (C1) substrates such as methanol are gaining increasing attention as cost-effective and environmentally friendly microbial feedstocks. Recent impressive metabolic engineering efforts to import C1 catabolic pathways into the non-methylotrophic bacterium Escherichia coli have led to synthetic strains growing on methanol as the sole carbon source. However, the growth rate and product yield in these strains remain inferior to native methylotrophs. Meanwhile, an ever-expanding genetic engineering toolbox is increasing the tractability of native C1 utilizers, raising the question of whether it is best to use an engineered strain or a native host for the microbial assimilation of C1 substrates. Here we provide perspective on this debate, using recent work in E. coli and the methylotrophic acetogen Eubacterium limosum as case studies.
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Affiliation(s)
- Patrick A Sanford
- Northeastern University, Department of Chemical Engineering, 360 Huntington Avenue, 223 Cullinane, United States
| | - Benjamin M Woolston
- Northeastern University, Department of Chemical Engineering, 360 Huntington Avenue, 223 Cullinane, United States.
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27
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García JL, Galán B. Integrating greenhouse gas capture and C1 biotechnology: a key challenge for circular economy. Microb Biotechnol 2021; 15:228-239. [PMID: 34905295 PMCID: PMC8719819 DOI: 10.1111/1751-7915.13991] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 11/27/2021] [Indexed: 12/02/2022] Open
Affiliation(s)
- José L García
- Environmental Biotechnology Laboratory, Department of Microbial and Plant Biotechnology, Centro de Investigaciones Biológicas Margarita Salas (CIB-MS, CSIC), Madrid, Spain
| | - Beatriz Galán
- Environmental Biotechnology Laboratory, Department of Microbial and Plant Biotechnology, Centro de Investigaciones Biológicas Margarita Salas (CIB-MS, CSIC), Madrid, Spain
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Flaiz M, Ludwig G, Bengelsdorf FR, Dürre P. Production of the biocommodities butanol and acetone from methanol with fluorescent FAST-tagged proteins using metabolically engineered strains of Eubacterium limosum. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:117. [PMID: 33971948 PMCID: PMC8111989 DOI: 10.1186/s13068-021-01966-2] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 04/29/2021] [Indexed: 05/12/2023]
Abstract
BACKGROUND The interest in using methanol as a substrate to cultivate acetogens increased in recent years since it can be sustainably produced from syngas and has the additional benefit of reducing greenhouse gas emissions. Eubacterium limosum is one of the few acetogens that can utilize methanol, is genetically accessible and, therefore, a promising candidate for the recombinant production of biocommodities from this C1 carbon source. Although several genetic tools are already available for certain acetogens including E. limosum, the use of brightly fluorescent reporter proteins is still limited. RESULTS In this study, we expanded the genetic toolbox of E. limosum by implementing the fluorescence-activating and absorption shifting tag (FAST) as a fluorescent reporter protein. Recombinant E. limosum strains that expressed the gene encoding FAST in an inducible and constitutive manner were constructed. Cultivation of these recombinant strains resulted in brightly fluorescent cells even under anaerobic conditions. Moreover, we produced the biocommodities butanol and acetone from methanol with recombinant E. limosum strains. Therefore, we used E. limosum cultures that produced FAST-tagged fusion proteins of the bifunctional acetaldehyde/alcohol dehydrogenase or the acetoacetate decarboxylase, respectively, and determined the fluorescence intensity and product concentrations during growth. CONCLUSIONS The addition of FAST as an oxygen-independent fluorescent reporter protein expands the genetic toolbox of E. limosum. Moreover, our results show that FAST-tagged fusion proteins can be constructed without negatively impacting the stability, functionality, and productivity of the resulting enzyme. Finally, butanol and acetone can be produced from methanol using recombinant E. limosum strains expressing genes encoding fluorescent FAST-tagged fusion proteins.
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Affiliation(s)
- Maximilian Flaiz
- Institute of Microbiology and Biotechnology, Ulm University, Albert-Einstein-Allee 11, 89081, Ulm, Germany.
| | - Gideon Ludwig
- Institute of Microbiology and Biotechnology, Ulm University, Albert-Einstein-Allee 11, 89081, Ulm, Germany
| | - Frank R Bengelsdorf
- Institute of Microbiology and Biotechnology, Ulm University, Albert-Einstein-Allee 11, 89081, Ulm, Germany
| | - Peter Dürre
- Institute of Microbiology and Biotechnology, Ulm University, Albert-Einstein-Allee 11, 89081, Ulm, Germany
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Weitz S, Hermann M, Linder S, Bengelsdorf FR, Takors R, Dürre P. Isobutanol Production by Autotrophic Acetogenic Bacteria. Front Bioeng Biotechnol 2021; 9:657253. [PMID: 33912549 PMCID: PMC8072342 DOI: 10.3389/fbioe.2021.657253] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 03/22/2021] [Indexed: 02/04/2023] Open
Abstract
Two different isobutanol synthesis pathways were cloned into and expressed in the two model acetogenic bacteria Acetobacterium woodii and Clostridium ljungdahlii. A. woodii is specialized on using CO2 + H2 gas mixtures for growth and depends on sodium ions for ATP generation by a respective ATPase and Rnf system. On the other hand, C. ljungdahlii grows well on syngas (CO + H2 + CO2 mixture) and depends on protons for energy conservation. The first pathway consisted of ketoisovalerate ferredoxin oxidoreductase (Kor) from Clostridium thermocellum and bifunctional aldehyde/alcohol dehydrogenase (AdhE2) from C. acetobutylicum. Three different kor gene clusters are annotated in C. thermocellum and were all tested. Only in recombinant A. woodii strains, traces of isobutanol could be detected. Additional feeding of ketoisovalerate increased isobutanol production to 2.9 mM under heterotrophic conditions using kor3 and to 1.8 mM under autotrophic conditions using kor2. In C. ljungdahlii, isobutanol could only be detected upon additional ketoisovalerate feeding under autotrophic conditions. kor3 proved to be the best suited gene cluster. The second pathway consisted of ketoisovalerate decarboxylase from Lactococcus lactis and alcohol dehydrogenase from Corynebacterium glutamicum. For increasing the carbon flux to ketoisovalerate, genes encoding ketol-acid reductoisomerase, dihydroxy-acid dehydratase, and acetolactate synthase from C. ljungdahlii were subcloned downstream of adhA. Under heterotrophic conditions, A. woodii produced 0.2 mM isobutanol and 0.4 mM upon additional ketoisovalerate feeding. Under autotrophic conditions, no isobutanol formation could be detected. Only upon additional ketoisovalerate feeding, recombinant A. woodii produced 1.5 mM isobutanol. With C. ljungdahlii, no isobutanol was formed under heterotrophic conditions and only 0.1 mM under autotrophic conditions. Additional feeding of ketoisovalerate increased these values to 1.5 mM and 0.6 mM, respectively. A further increase to 2.4 mM and 1 mM, respectively, could be achieved upon inactivation of the ilvE gene in the recombinant C. ljungdahlii strain. Engineering the coenzyme specificity of IlvC of C. ljungdahlii from NADPH to NADH did not result in improved isobutanol production.
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Affiliation(s)
- Sandra Weitz
- Institut für Mikrobiologie und Biotechnologie, Universität Ulm, Ulm, Germany
| | - Maria Hermann
- Institut für Bioverfahrenstechnik, Universität Stuttgart, Stuttgart, Germany
| | - Sonja Linder
- Institut für Mikrobiologie und Biotechnologie, Universität Ulm, Ulm, Germany
| | - Frank R Bengelsdorf
- Institut für Mikrobiologie und Biotechnologie, Universität Ulm, Ulm, Germany
| | - Ralf Takors
- Institut für Bioverfahrenstechnik, Universität Stuttgart, Stuttgart, Germany
| | - Peter Dürre
- Institut für Mikrobiologie und Biotechnologie, Universität Ulm, Ulm, Germany
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