Reconstruction and metabolic profiling of the genome-scale metabolic network model of Pseudomonas stutzeri A1501
Pseudomonas stutzeri A1501 is a non-fluorescent denitrifying bacteria that belongs to the gram-negative bacterial group. As a prominent strain in the fields of agriculture and bioengineering, there is still a lack of comprehensive understanding regarding its metabolic capabilities, specifically in t...
| Main Authors: | , , , , , , , |
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| Format: | Article |
| Language: | English |
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KeAi Communications Co., Ltd.
2023-12-01
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| Series: | Synthetic and Systems Biotechnology |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2405805X23000832 |
| _version_ | 1797372952356847616 |
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| author | Qianqian Yuan Fan Wei Xiaogui Deng Aonan Li Zhenkun Shi Zhitao Mao Feiran Li Hongwu Ma |
| author_facet | Qianqian Yuan Fan Wei Xiaogui Deng Aonan Li Zhenkun Shi Zhitao Mao Feiran Li Hongwu Ma |
| author_sort | Qianqian Yuan |
| collection | DOAJ |
| description | Pseudomonas stutzeri A1501 is a non-fluorescent denitrifying bacteria that belongs to the gram-negative bacterial group. As a prominent strain in the fields of agriculture and bioengineering, there is still a lack of comprehensive understanding regarding its metabolic capabilities, specifically in terms of central metabolism and substrate utilization. Therefore, further exploration and extensive studies are required to gain a detailed insight into these aspects. This study reconstructed a genome-scale metabolic network model for P. stutzeri A1501 and conducted extensive curations, including correcting energy generation cycles, respiratory chains, and biomass composition. The final model, iQY1018, was successfully developed, covering more genes and reactions and having higher prediction accuracy compared with the previously published model iPB890. The substrate utilization ability of 71 carbon sources was investigated by BIOLOG experiment and was utilized to validate the model quality. The model prediction accuracy of substrate utilization for P. stutzeri A1501 reached 90 %. The model analysis revealed its new ability in central metabolism and predicted that the strain is a suitable chassis for the production of Acetyl CoA-derived products. This work provides an updated, high-quality model of P. stutzeri A1501for further research and will further enhance our understanding of the metabolic capabilities. |
| first_indexed | 2024-03-08T18:43:14Z |
| format | Article |
| id | doaj.art-bb96ab67afe0470a93270be31fe06eb0 |
| institution | Directory Open Access Journal |
| issn | 2405-805X |
| language | English |
| last_indexed | 2024-03-08T18:43:14Z |
| publishDate | 2023-12-01 |
| publisher | KeAi Communications Co., Ltd. |
| record_format | Article |
| series | Synthetic and Systems Biotechnology |
| spelling | doaj.art-bb96ab67afe0470a93270be31fe06eb02023-12-29T04:45:38ZengKeAi Communications Co., Ltd.Synthetic and Systems Biotechnology2405-805X2023-12-0184688696Reconstruction and metabolic profiling of the genome-scale metabolic network model of Pseudomonas stutzeri A1501Qianqian Yuan0Fan Wei1Xiaogui Deng2Aonan Li3Zhenkun Shi4Zhitao Mao5Feiran Li6Hongwu Ma7Biodesign Center, Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China; National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, ChinaBiodesign Center, Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China; University of Chinese Academy of Sciences, Beijing, 100049, China; National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, ChinaBiodesign Center, Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China; National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China; School of Biological Engineering, Tianjin University of Science and Technology, Tianjin, ChinaBiodesign Center, Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China; National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China; School of Biological Engineering, Tianjin University of Science and Technology, Tianjin, ChinaBiodesign Center, Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China; National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, ChinaBiodesign Center, Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China; National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, ChinaInstitute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, China; Corresponding author.Biodesign Center, Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China; National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China; Corresponding author. Biodesign Center, Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.Pseudomonas stutzeri A1501 is a non-fluorescent denitrifying bacteria that belongs to the gram-negative bacterial group. As a prominent strain in the fields of agriculture and bioengineering, there is still a lack of comprehensive understanding regarding its metabolic capabilities, specifically in terms of central metabolism and substrate utilization. Therefore, further exploration and extensive studies are required to gain a detailed insight into these aspects. This study reconstructed a genome-scale metabolic network model for P. stutzeri A1501 and conducted extensive curations, including correcting energy generation cycles, respiratory chains, and biomass composition. The final model, iQY1018, was successfully developed, covering more genes and reactions and having higher prediction accuracy compared with the previously published model iPB890. The substrate utilization ability of 71 carbon sources was investigated by BIOLOG experiment and was utilized to validate the model quality. The model prediction accuracy of substrate utilization for P. stutzeri A1501 reached 90 %. The model analysis revealed its new ability in central metabolism and predicted that the strain is a suitable chassis for the production of Acetyl CoA-derived products. This work provides an updated, high-quality model of P. stutzeri A1501for further research and will further enhance our understanding of the metabolic capabilities.http://www.sciencedirect.com/science/article/pii/S2405805X23000832 |
| spellingShingle | Qianqian Yuan Fan Wei Xiaogui Deng Aonan Li Zhenkun Shi Zhitao Mao Feiran Li Hongwu Ma Reconstruction and metabolic profiling of the genome-scale metabolic network model of Pseudomonas stutzeri A1501 Synthetic and Systems Biotechnology |
| title | Reconstruction and metabolic profiling of the genome-scale metabolic network model of Pseudomonas stutzeri A1501 |
| title_full | Reconstruction and metabolic profiling of the genome-scale metabolic network model of Pseudomonas stutzeri A1501 |
| title_fullStr | Reconstruction and metabolic profiling of the genome-scale metabolic network model of Pseudomonas stutzeri A1501 |
| title_full_unstemmed | Reconstruction and metabolic profiling of the genome-scale metabolic network model of Pseudomonas stutzeri A1501 |
| title_short | Reconstruction and metabolic profiling of the genome-scale metabolic network model of Pseudomonas stutzeri A1501 |
| title_sort | reconstruction and metabolic profiling of the genome scale metabolic network model of pseudomonas stutzeri a1501 |
| url | http://www.sciencedirect.com/science/article/pii/S2405805X23000832 |
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