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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Abstract
Despite our continuous improvement in understanding antibiotic resistance, the interplay between natural selection of resistance mutations and the environment remains unclear. To investigate the role of bacterial metabolism in constraining the evolution of antibiotic resistance, we evolved Escherichia coli growing on glycolytic or gluconeogenic carbon sources to the selective pressure of three different antibiotics. Profiling more than 500 intracellular and extracellular putative metabolites in 190 evolved populations revealed that carbon and energy metabolism strongly constrained the evolutionary trajectories, both in terms of speed and mode of resistance acquisition. To interpret and explore the space of metabolome changes, we developed a novel constraint‐based modeling approach using the concept of shadow prices. This analysis, together with genome resequencing of resistant populations, identified condition‐dependent compensatory mechanisms of antibiotic resistance, such as the shift from respiratory to fermentative metabolism of glucose upon overexpression of efflux pumps. Moreover, metabolome‐based predictions revealed emerging weaknesses in resistant strains, such as the hypersensitivity to fosfomycin of ampicillin‐resistant strains. Overall, resolving metabolic adaptation throughout antibiotic‐driven evolutionary trajectories opens new perspectives in the fight against emerging antibiotic resistance.
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Affiliation(s)
- Mattia Zampieri
- Institute of Molecular Systems Biology, ETH Zürich, Zürich, Switzerland
| | - Tim Enke
- Institute of Molecular Systems Biology, ETH Zürich, Zürich, Switzerland.,Institute of Biogeochemistry and Pollutant Dynamics (IBP), ETH Zürich, Zürich, Switzerland
| | - Victor Chubukov
- Institute of Molecular Systems Biology, ETH Zürich, Zürich, Switzerland
| | - Vito Ricci
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK
| | - Laura Piddock
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK
| | - Uwe Sauer
- Institute of Molecular Systems Biology, ETH Zürich, Zürich, Switzerland
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Bordbar A, Nagarajan H, Lewis NE, Latif H, Ebrahim A, Federowicz S, Schellenberger J, Palsson BO. Minimal metabolic pathway structure is consistent with associated biomolecular interactions. Mol Syst Biol 2014; 10:737. [PMID: 24987116 PMCID: PMC4299494 DOI: 10.15252/msb.20145243] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Pathways are a universal paradigm for functionally describing cellular processes. Even though advances in high-throughput data generation have transformed biology, the core of our biological understanding, and hence data interpretation, is still predicated on human-defined pathways. Here, we introduce an unbiased, pathway structure for genome-scale metabolic networks defined based on principles of parsimony that do not mimic canonical human-defined textbook pathways. Instead, these minimal pathways better describe multiple independent pathway-associated biomolecular interaction datasets suggesting a functional organization for metabolism based on parsimonious use of cellular components. We use the inherent predictive capability of these pathways to experimentally discover novel transcriptional regulatory interactions in Escherichia coli metabolism for three transcription factors, effectively doubling the known regulatory roles for Nac and MntR. This study suggests an underlying and fundamental principle in the evolutionary selection of pathway structures; namely, that pathways may be minimal, independent, and segregated.
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Affiliation(s)
- Aarash Bordbar
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Harish Nagarajan
- Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA, USA
| | - Nathan E Lewis
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA Department of Pediatrics, University of California San Diego School of Medicine, La Jolla, CA, USA Wyss Institute for Biologically Inspired Engineering and Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Haythem Latif
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Ali Ebrahim
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Stephen Federowicz
- Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA, USA
| | - Jan Schellenberger
- Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA, USA
| | - Bernhard O Palsson
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA, USA Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
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