Addressing genome scale design tradeoffs in Pseudomonas putida for bioconversion of an aromatic carbon source

• Published in: NPJ systems biology and applications Vol. 11; no. 1; pp. 8 - 13
• Main Authors: Banerjee, Deepanwita, Menasalvas, Javier, Chen, Yan, Gin, Jennifer W., Baidoo, Edward E. K., Petzold, Christopher J., Eng, Thomas, Mukhopadhyay, Aindrila
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 14.01.2025; Nature Publishing Group; Springer Nature; Nature Portfolio
• Subjects: 631/553/2690; 631/61/318; Bioconversion; Bioinformatics; Biomedical and Life Sciences; Carbon; Carbon sources; Citric Acid Cycle - genetics; Computational Biology/Bioinformatics; Computer Appl. in Life Sciences; Coumaric Acids - metabolism; Enzymatic activity; Enzymes; Fumarase; Fumarate Hydratase - genetics; Fumarate Hydratase - metabolism; Gene Deletion; Genetic Engineering; Genome, Bacterial; Genomes; Glutamine; Glutamine - metabolism; Life Sciences; Metabolic engineering; Metabolism; Piperidones - metabolism; Proteomics; Pseudomonas putida; Pseudomonas putida - genetics; Pseudomonas putida - growth & development; Pseudomonas putida - metabolism; Sensitivity analysis; Syntrophism; Systems Biology

Genome-scale metabolic models (GSMM) are commonly used to identify gene deletion sets that result in growth coupling and pairing product formation with substrate utilization and can improve strain performance beyond levels typically accessible using traditional strain engineering approaches. However...