Metabolic reconstruction of Pseudomonas chlororaphis ATCC 9446 to understand its metabolic potential as a phenazine-1-carboxamide-producing strain

• Published in: Applied microbiology and biotechnology Vol. 104; no. 23; pp. 10119 - 10132
• Main Authors: Moreno-Avitia, Fabián, Utrilla, José, Bolívar, Francisco, Nogales, Juan, Escalante, Adelfo
• Format: Journal Article
• Language: English
• Published: Berlin/Heidelberg Springer Berlin Heidelberg 01-12-2020; Springer; Springer Nature B.V
• Subjects: Amides; Biomedical and Life Sciences; Biotechnology; Carbon; Carbon sources; Cellular stress response; Denitrification; Fatty acids; Fluxes; Galactose; Genomes; Genomics; Glutamine; Glycerol; Hydrogen Peroxide; Life Sciences; Mannose; Metabolic networks; Metabolism; Microbial Genetics and Genomics; Microbial metabolism; Microbiology; Network analysis; Observations; Optimization; Organisms; Phenazine; Phenazines; Phenotypes; Physiological aspects; Plant growth; Proteomics; Pseudomonas; Pseudomonas - genetics; Pseudomonas chlororaphis; Pseudomonas chlororaphis - genetics; Scale models; Sucrose; Sugar; Transcriptomics; Trehalose; Mexico; Phenazine-1-carboxamide; Metabolic engineering; Genome-scale model; Metabolic reconstruction; Pseudomonas chlororaphis
• ISSN: 0175-7598; 1432-0614
• DOI: 10.1007/s00253-020-10913-4

Pseudomonas chlororaphis
is a plant-associated bacterium with reported antagonistic activity against different organisms and plant growth–promoting properties.
P. chlororaphis
possesses exciting biotechnological features shared with another
Pseudomonas
with a nonpathogenic phenotype. Part of the antagonistic role of
P. chlororaphis
is due to its production of a wide variety of phenazines. To expand the knowledge of the metabolic traits of this organism, we constructed the first experimentally validated genome-scale model of
P. chlororaphis
ATCC 9446, containing 1267 genes and 2289 reactions, and analyzed strategies to maximize its potential for the production of phenazine-1-carboxamide (PCN). The resulting model also describes the capability of
P. chlororaphis
to carry out the denitrification process and its ability to consume sucrose (Scr), trehalose, mannose, and galactose as carbon sources. Additionally, metabolic network analysis suggested fatty acids as the best carbon source for PCN production. Moreover, the optimization of PCN production was performed with glucose and glycerol. The optimal PCN production phenotype requires an increased carbon flux in TCA and glutamine synthesis. Our simulations highlight the intrinsic H
2
O
2
flux associated with PCN production, which may generate cellular stress in an overproducing strain. These results suggest that an improved antioxidative strategy could lead to optimal performance of phenazine-producing strains of
P. chlororaphis
.
Key points
• This is the first publication of a metabolic model for a strain of P. chlororaphis.
• Genome-scale model is worthy tool to increase the knowledge of a non model organism.
• Fluxes simulations indicate a possible effect of H
2
O
2
on phenazines production.
• P. chlororaphis can be a suitable model for a wide variety of compounds.