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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...

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Autores principales: Yuan, Qianqian, Wei, Fan, Deng, Xiaogui, Li, Aonan, Shi, Zhenkun, Mao, Zhitao, Li, Feiran, Ma, Hongwu
Formato: Online Artículo Texto
Lenguaje:English
Publicado: KeAi Publishing 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10624960/
https://www.ncbi.nlm.nih.gov/pubmed/37927897
http://dx.doi.org/10.1016/j.synbio.2023.10.001
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author Yuan, Qianqian
Wei, Fan
Deng, Xiaogui
Li, Aonan
Shi, Zhenkun
Mao, Zhitao
Li, Feiran
Ma, Hongwu
author_facet Yuan, Qianqian
Wei, Fan
Deng, Xiaogui
Li, Aonan
Shi, Zhenkun
Mao, Zhitao
Li, Feiran
Ma, Hongwu
author_sort Yuan, Qianqian
collection PubMed
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.
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spelling pubmed-106249602023-11-05 Reconstruction and metabolic profiling of the genome-scale metabolic network model of Pseudomonas stutzeri A1501 Yuan, Qianqian Wei, Fan Deng, Xiaogui Li, Aonan Shi, Zhenkun Mao, Zhitao Li, Feiran Ma, Hongwu Synth Syst Biotechnol Original Research Article 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. KeAi Publishing 2023-10-20 /pmc/articles/PMC10624960/ /pubmed/37927897 http://dx.doi.org/10.1016/j.synbio.2023.10.001 Text en © 2023 The Authors https://creativecommons.org/licenses/by-nc-nd/4.0/This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).
spellingShingle Original Research Article
Yuan, Qianqian
Wei, Fan
Deng, Xiaogui
Li, Aonan
Shi, Zhenkun
Mao, Zhitao
Li, Feiran
Ma, Hongwu
Reconstruction and metabolic profiling of the genome-scale metabolic network model of Pseudomonas stutzeri A1501
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
topic Original Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10624960/
https://www.ncbi.nlm.nih.gov/pubmed/37927897
http://dx.doi.org/10.1016/j.synbio.2023.10.001
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