PDF(Pubmed)
Abstract：
BACKGROUND: Pseudomonas putida S12 is a gram-negative bacterium renowned for its high tolerance to organic solvents and metabolic versatility, making it attractive for various applications, including bioremediation and the production of aromatic compounds, bioplastics, biofuels, and value-added compounds. However, a metabolic model of S12 has yet to be developed.
RESULTS: In this study, we present a comprehensive and highly curated genome-scale metabolic network model of S12 (iSH1474), containing 1,474 genes, 1,436 unique metabolites, and 2,938 metabolic reactions. The model was constructed by leveraging existing metabolic models and conducting comparative analyses of genomes and phenomes. Approximately 2,000 different phenotypes were measured for S12 and its closely related KT2440 strain under various nutritional and environmental conditions. These phenotypic data, combined with the reported experimental data, were used to refine and validate the reconstruction. Model predictions quantitatively agreed well with in vivo flux measurements and the batch cultivation of S12, which demonstrated that iSH1474 accurately represents the metabolic capabilities of S12. Furthermore, the model was simulated to investigate the maximum theoretical metabolic capacity of S12 growing on toxic organic solvents.
CONCLUSIONS: iSH1474 represents a significant advancement in our understanding of the cellular metabolism of P. putida S12. The combined results of metabolic simulation and comparative genome and phenome analyses identified the genetic and metabolic determinants of the characteristic phenotypes of S12. This study could accelerate the development of this versatile organism as an efficient cell factory for various biotechnological applications.
RESULTS: In this study, we present a comprehensive and highly curated genome-scale metabolic network model of S12 (iSH1474), containing 1,474 genes, 1,436 unique metabolites, and 2,938 metabolic reactions. The model was constructed by leveraging existing metabolic models and conducting comparative analyses of genomes and phenomes. Approximately 2,000 different phenotypes were measured for S12 and its closely related KT2440 strain under various nutritional and environmental conditions. These phenotypic data, combined with the reported experimental data, were used to refine and validate the reconstruction. Model predictions quantitatively agreed well with in vivo flux measurements and the batch cultivation of S12, which demonstrated that iSH1474 accurately represents the metabolic capabilities of S12. Furthermore, the model was simulated to investigate the maximum theoretical metabolic capacity of S12 growing on toxic organic solvents.
CONCLUSIONS: iSH1474 represents a significant advancement in our understanding of the cellular metabolism of P. putida S12. The combined results of metabolic simulation and comparative genome and phenome analyses identified the genetic and metabolic determinants of the characteristic phenotypes of S12. This study could accelerate the development of this versatile organism as an efficient cell factory for various biotechnological applications.
摘要：
背景：恶臭假单胞菌S12是一种革兰氏阴性菌，以对有机溶剂的高耐受性和代谢多功能性而闻名，使其对各种应用具有吸引力，包括生物修复和芳香族化合物的生产，生物塑料,生物燃料,和增值化合物。然而,S12的代谢模型尚未开发。
结果：在这项研究中，我们提出了一个全面的、高度策划的S12(iSH1474)基因组尺度代谢网络模型，含有1474个基因，1,436种独特的代谢物，和2,938个代谢反应。该模型是通过利用现有的代谢模型并对基因组和表型进行比较分析来构建的。在各种营养和环境条件下，对S12及其密切相关的KT2440菌株测量了大约2,000种不同的表型。这些表型数据，结合报道的实验数据，用于改进和验证重建。模型预测在数量上与体内通量测量和S12的分批培养非常吻合，这表明iSH1474准确地代表了S12的代谢能力。此外，模拟了S12在有毒有机溶剂上生长的最大理论代谢能力。
结论：iSH1474代表了我们对恶臭假单胞菌S12细胞代谢的理解的重大进展。代谢模拟以及比较基因组和表型分析的综合结果确定了S12特征表型的遗传和代谢决定因素。这项研究可以加速这种多功能生物的发展，成为各种生物技术应用的有效细胞工厂。
结果：在这项研究中，我们提出了一个全面的、高度策划的S12(iSH1474)基因组尺度代谢网络模型，含有1474个基因，1,436种独特的代谢物，和2,938个代谢反应。该模型是通过利用现有的代谢模型并对基因组和表型进行比较分析来构建的。在各种营养和环境条件下，对S12及其密切相关的KT2440菌株测量了大约2,000种不同的表型。这些表型数据，结合报道的实验数据，用于改进和验证重建。模型预测在数量上与体内通量测量和S12的分批培养非常吻合，这表明iSH1474准确地代表了S12的代谢能力。此外，模拟了S12在有毒有机溶剂上生长的最大理论代谢能力。
结论：iSH1474代表了我们对恶臭假单胞菌S12细胞代谢的理解的重大进展。代谢模拟以及比较基因组和表型分析的综合结果确定了S12特征表型的遗传和代谢决定因素。这项研究可以加速这种多功能生物的发展，成为各种生物技术应用的有效细胞工厂。
