Reconstruction and metabolic profiling of the genome-scale metabolic network model of Pseudomonas stutzeri A1501

Qianqian Yuan; Fan Wei; Xiaogui Deng; Aonan Li; Zhenkun Shi; Zhitao Mao; Feiran Li; Hongwu Ma

doi:10.1016/j.synbio.2023.10.001

Reconstruction and metabolic profiling of the genome-scale metabolic network model of Pseudomonas stutzeri A1501

Synth Syst Biotechnol. 2023 Oct 20;8(4):688-696. doi: 10.1016/j.synbio.2023.10.001. eCollection 2023 Dec.

Authors

Qianqian Yuan^{1

2}, Fan Wei^{1

3

2}, Xiaogui Deng^{1

2

4}, Aonan Li^{1

2

4}, Zhenkun Shi^{1

2}, Zhitao Mao^{1

2}, Feiran Li⁵, Hongwu Ma^{1

2}

Affiliations

¹ Biodesign Center, Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.
² National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China.
³ University of Chinese Academy of Sciences, Beijing, 100049, China.
⁴ School of Biological Engineering, Tianjin University of Science and Technology, Tianjin, China.
⁵ Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, China.

Abstract

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.