A reconciliation of genome-scale metabolic network model of Zymomonas mobilis ZM4

• Published in: Scientific reports Vol. 10; no. 1; p. 7782
• Main Authors: Nouri, Hoda, Fouladiha, Hamideh, Moghimi, Hamid, Marashi, Sayed-Amir
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 08-05-2020; Nature Publishing Group
• Subjects: 45/41; 45/43; 631/553/2695; 631/553/318; 631/61/318; Biotechnology; Computational Biology; Computer applications; Fermentation; Gene expression; Genome, Bacterial; Genomes; Genomics - methods; Humanities and Social Sciences; Metabolic Engineering; Metabolic networks; Metabolic Networks and Pathways; Metabolism; Metabolites; Models, Biological; multidisciplinary; Reproducibility of Results; Science; Science (multidisciplinary); Workflow; Zymomonas - genetics; Zymomonas - metabolism; Zymomonas mobilis
• ISSN: 2045-2322; 2045-2322
• DOI: 10.1038/s41598-020-64721-x

Zymomonas mobilis
ZM4 has recently been used for a variety of biotechnological purposes. To rationally enhance its metabolic performance, a reliable genome-scale metabolic network model (GEM) of this organism is required. To this end, we reconstructed a genome-scale metabolic model (
i
HN446) for
Z. mobilis
, which involves 446 genes, 859 reactions, and 894 metabolites. We started by first reconciling the existing GEMs previously constructed for
Z. mobilis
to obtain a draft network. Next, recent gene annotations, up-to-date literature, physiological data and biochemical databases were used to upgrade the network. Afterward, the draft network went through a curative and iterative process of gap-filling by computational tools and manual refinement. The final model was evaluated using experimental data and literature information. We next applied this model as a platform for analyzing the links between transcriptome-flux and transcriptome-metabolome. We found that experimental observations were in agreement with the predicted results from our final GEM. Taken together, this comprehensive model (
i
HN446) can be utilized for studying metabolism in
Z. mobilis
and finding rational targets for metabolic engineering applications.