System-level characterization of engineered and evolved formatotrophic E. coli strains
One-carbon compounds, such as formate, are promising and sustainable feedstocks for microbial bioproduction of fuels and chemicals. Growth of Escherichia coli on formate was recently achieved by introducing the reductive glycine pathway (rGlyP) into its genome, which is theoretically the most energy...
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| Format: | Article |
| Language: | English |
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KeAi Communications Co., Ltd.
2025-06-01
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| Series: | Synthetic and Systems Biotechnology |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S2405805X25000341 |
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| author | Suzan Yilmaz Boas Kanis Rensco A.H. Hogers Sara Benito-Vaquerizo Jörg Kahnt Timo Glatter Beau Dronsella Tobias J. Erb Maria Suarez-Diez Nico J. Claassens |
| author_facet | Suzan Yilmaz Boas Kanis Rensco A.H. Hogers Sara Benito-Vaquerizo Jörg Kahnt Timo Glatter Beau Dronsella Tobias J. Erb Maria Suarez-Diez Nico J. Claassens |
| author_sort | Suzan Yilmaz |
| collection | DOAJ |
| description | One-carbon compounds, such as formate, are promising and sustainable feedstocks for microbial bioproduction of fuels and chemicals. Growth of Escherichia coli on formate was recently achieved by introducing the reductive glycine pathway (rGlyP) into its genome, which is theoretically the most energy-efficient aerobic formate assimilation pathway. While adaptive laboratory evolution was used to enhance the growth rate and biomass yield significantly, still the best performing formatotrophic E. coli strain did not approach the theoretical optimal biomass yield of the rGlyP. In this study, we investigated these previously engineered formatotrophic E. coli strains to find out why the biomass yield was sub-optimal and how it may be improved. Through a combination of metabolic modelling, genomic and proteomic analysis, we identified several potential metabolic bottlenecks and future targets for optimization. This study also reveals further insights in the evolutionary mutations and related changes in proteome allocation that supported the already substantially improved growth of formatotrophic E. coli strains. This systems-level analysis provides key insights to realize high-yield, fast growing formatotrophic strains for future bioproduction. |
| format | Article |
| id | doaj-art-a8d02f2c9cec4cbcb50d0041e587b158 |
| institution | OA Journals |
| issn | 2405-805X |
| language | English |
| publishDate | 2025-06-01 |
| publisher | KeAi Communications Co., Ltd. |
| record_format | Article |
| series | Synthetic and Systems Biotechnology |
| spelling | doaj-art-a8d02f2c9cec4cbcb50d0041e587b1582025-08-20T02:07:57ZengKeAi Communications Co., Ltd.Synthetic and Systems Biotechnology2405-805X2025-06-0110265066610.1016/j.synbio.2025.03.001System-level characterization of engineered and evolved formatotrophic E. coli strainsSuzan Yilmaz0Boas Kanis1Rensco A.H. Hogers2Sara Benito-Vaquerizo3Jörg Kahnt4Timo Glatter5Beau Dronsella6Tobias J. Erb7Maria Suarez-Diez8Nico J. Claassens9Laboratory of Microbiology, Wageningen University, Wageningen, the NetherlandsLaboratory of Systems and Synthetic Biology, Wageningen University, Wageningen, the NetherlandsLaboratory of Systems and Synthetic Biology, Wageningen University, Wageningen, the NetherlandsLaboratory of Systems and Synthetic Biology, Wageningen University, Wageningen, the Netherlands; Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, GermanyCore Facility for Mass Spectrometry and Proteomics, Max Planck Institute for Terrestrial Microbiology, Marburg, GermanyCore Facility for Mass Spectrometry and Proteomics, Max Planck Institute for Terrestrial Microbiology, Marburg, GermanyBiochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Marburg, GermanyBiochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany; Center for Synthetic Microbiology, Marburg, GermanyLaboratory of Systems and Synthetic Biology, Wageningen University, Wageningen, the NetherlandsLaboratory of Microbiology, Wageningen University, Wageningen, the Netherlands; Corresponding author.One-carbon compounds, such as formate, are promising and sustainable feedstocks for microbial bioproduction of fuels and chemicals. Growth of Escherichia coli on formate was recently achieved by introducing the reductive glycine pathway (rGlyP) into its genome, which is theoretically the most energy-efficient aerobic formate assimilation pathway. While adaptive laboratory evolution was used to enhance the growth rate and biomass yield significantly, still the best performing formatotrophic E. coli strain did not approach the theoretical optimal biomass yield of the rGlyP. In this study, we investigated these previously engineered formatotrophic E. coli strains to find out why the biomass yield was sub-optimal and how it may be improved. Through a combination of metabolic modelling, genomic and proteomic analysis, we identified several potential metabolic bottlenecks and future targets for optimization. This study also reveals further insights in the evolutionary mutations and related changes in proteome allocation that supported the already substantially improved growth of formatotrophic E. coli strains. This systems-level analysis provides key insights to realize high-yield, fast growing formatotrophic strains for future bioproduction.http://www.sciencedirect.com/science/article/pii/S2405805X25000341Escherichia coliMetabolic modellingC1-assimilationFormateReductive glycine pathway |
| spellingShingle | Suzan Yilmaz Boas Kanis Rensco A.H. Hogers Sara Benito-Vaquerizo Jörg Kahnt Timo Glatter Beau Dronsella Tobias J. Erb Maria Suarez-Diez Nico J. Claassens System-level characterization of engineered and evolved formatotrophic E. coli strains Synthetic and Systems Biotechnology Escherichia coli Metabolic modelling C1-assimilation Formate Reductive glycine pathway |
| title | System-level characterization of engineered and evolved formatotrophic E. coli strains |
| title_full | System-level characterization of engineered and evolved formatotrophic E. coli strains |
| title_fullStr | System-level characterization of engineered and evolved formatotrophic E. coli strains |
| title_full_unstemmed | System-level characterization of engineered and evolved formatotrophic E. coli strains |
| title_short | System-level characterization of engineered and evolved formatotrophic E. coli strains |
| title_sort | system level characterization of engineered and evolved formatotrophic e coli strains |
| topic | Escherichia coli Metabolic modelling C1-assimilation Formate Reductive glycine pathway |
| url | http://www.sciencedirect.com/science/article/pii/S2405805X25000341 |
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