Department of Bioscience and Biotechnology, Konkuk University, Seoul, 05029, Republic of Korea.
BMC Genomics. 2024 Jan 16;25(1):63. doi: 10.1186/s12864-023-09940-y.
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.
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.
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.
铜绿假单胞菌 S12 是一种革兰氏阴性细菌，以其对有机溶剂的高耐受性和代谢多功能性而闻名，使其成为各种应用的理想选择，包括生物修复和芳香族化合物、生物塑料、生物燃料和增值化合物的生产。然而，S12 的代谢模型尚未开发。
在这项研究中，我们提出了 S12（iSH1474）的综合和高度精细化的全基因组代谢网络模型，包含 1474 个基因、1436 个独特代谢物和 2938 个代谢反应。该模型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。大约 2000 种不同的表型被测量为 S12 和其密切相关的 KT2440 菌株在各种营养和环境条件下。这些表型数据与报告的实验数据相结合，用于精炼和验证重建。模型预测与体内通量测量和 S12 的分批培养定量吻合良好，这表明 iSH1474 准确地代表了 S12 的代谢能力。此外，该模型被模拟以研究 S12 在有毒有机溶剂上生长的最大理论代谢能力。
iSH1474 代表了我们对铜绿假单胞菌 S12 细胞代谢的理解的重大进展。代谢模拟和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体的发展，使其成为各种生物技术应用的高效细胞工厂。
