Construction and application of the genome-scale metabolic model of Streptomyces radiopugnans

Zhidong Zhang; Qi Guo; Jinyi Qian; Chao Ye; He Huang

doi:10.3389/fbioe.2023.1108412

Construction and application of the genome-scale metabolic model of Streptomyces radiopugnans

Front Bioeng Biotechnol. 2023 Feb 17:11:1108412. doi: 10.3389/fbioe.2023.1108412. eCollection 2023.

Authors

Zhidong Zhang^{1

2}, Qi Guo¹, Jinyi Qian³, Chao Ye³, He Huang^{1

3}

Affiliations

¹ College of Biotechnology and Pharmaceutical Engineering, Nanjing Technology University, Nanjing, China.
² Institute of Microbiology, Xinjiang Academy of Agricultural Sciences, Urumqi, China.
³ School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, China.

Abstract

Geosmin is one of the most common earthy-musty odor compounds, which is mainly produced by Streptomyces. Streptomyces radiopugnans was screened in radiation-polluted soil, which has the potential to overproduce geosmin. However, due to the complex cellular metabolism and regulation mechanism, the phenotypes of S. radiopugnans were hard to investigate. A genome-scale metabolic model of S. radiopugnans named iZDZ767 was constructed. Model iZDZ767 involved 1,411 reactions, 1,399 metabolites, and 767 genes; its gene coverage was 14.1%. Model iZDZ767 could grow on 23 carbon sources and five nitrogen sources, which achieved 82.1% and 83.3% prediction accuracy, respectively. For the essential gene prediction, the accuracy was 97.6%. According to the simulation of model iZDZ767, D-glucose and urea were the best for geosmin fermentation. The culture condition optimization experiments proved that with D-glucose as the carbon source and urea as the nitrogen source (4 g/L), geosmin production could reach 581.6 ng/L. Using the OptForce algorithm, 29 genes were identified as the targets of metabolic engineering modification. With the help of model iZDZ767, the phenotypes of S. radiopugnans could be well resolved. The key targets for geosmin overproduction could also be identified efficiently.

Keywords: Streptomyces radiopugnans; culture condition optimization; genome-scale metabolic model; geosmin; metabolic engineering.

Grants and funding

This work was supported by the National Natural Science Foundation of China (32060004), the Xinjiang Academy of Agricultural Sciences Science and technology innovation key cultivation project (xjkcpy-2021002, xjkcpy-2022004), the Third Xinjiang Scientific Expedition Program (2022xjkk1200), and the “Outstanding Youth Fund” of Xinjiang Natural Science Foundation (2022D01E19).