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
• ISSN: 2056-7189; 2056-7189
• DOI: 10.1038/s41540-024-00480-z

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, sustainable feedstocks pose a challenge due to incomplete high-resolution metabolic data for non-canonical carbon sources required to curate GSMM and identify implementable designs. Here we address a four-gene deletion design in the Pseudomonas putida KT2440 strain for the lignin-derived non-sugar carbon source, p -coumarate ( p -CA), that proved challenging to implement. We examine the performance of the fully implemented design for p- coumarate to glutamine, a useful biomanufacturing intermediate. In this study glutamine is then converted to indigoidine, an alternative sustainable pigment and a model heterologous product that is commonly used to colorimetrically quantify glutamine concentration. Through proteomics, promoter-variation, and growth characterization of a fully implemented gene deletion design, we provide evidence that aromatic catabolism in the completed design is rate-limited by fumarase hydratase (FUM) enzyme activity in the citrate cycle and requires careful optimization of another fumarate hydratase protein (PP_0897) expression to achieve growth and production. A double sensitivity analysis also confirmed a strict requirement for fumarate hydratase activity in the strain where all genes in the growth coupling design have been implemented. Metabolic cross-feeding experiments were used to examine the impact of complete removal of the fumarase hydratase reaction and revealed an unanticipated nutrient requirement, suggesting additional functions for this enzyme. While a complete implementation of the design was achieved, this study highlights the challenge of completely inactivating metabolic reactions encoded by under-characterized proteins, especially in the context of multi-gene edits.