Work

Dissecting Metabolic Rewiring and Gene-Metabolite Interactions by Utilizing Untargeted Metabolomics and Single-Gene Knockouts in the Model Microorganism E. coli

Year: 2026

Type: article

Abstract: High Resolution Image Download MS PowerPoint Slide Central carbon metabolism, comprising glycolysis, the tricarboxylic acid (TCA) cycle, and the pentose phosphate pathway (PPP), is essential for Escherichia coli survival and growth. While disruptions in these pathways are known to affect cellular physiology, the system-wide metabolite-level consequences of single-gene knockouts remain incompletely understood. Using untargeted LC-MS metabolomics, we systematically profiled E. coli knockouts of TCA core enzymes, isoforms, subunits, bypass routes, and TCA-associated pathways. Core TCA knockouts separated into two major metabolic clusters, with cluster 1 strains displaying strong divergence in amino acid metabolism and cluster 2 retaining partial similarity to the parent strain. Isoform-specific deletions revealed differential roles of aconitases (Δ acnA vs Δ acnB ) and fumarases (Δ fumA vs Δ fumC ), while subunit knockouts of 2-oxoglutarate dehydrogenase (Δ sucA, Δ sucB ) and succinate dehydrogenase (Δ sdhA-D ) produced localized but distinct metabolite shifts, particularly around glutamate- and 2-oxoglutarate-linked metabolism. Bypass enzyme deletions (Δ aceA, Δ aceB, Δ glcB, and Δ maeB ) disrupted carbohydrate- and redox-related metabolites, underscoring their role as metabolic safety nets. Importantly, knockouts also triggered off-target effects in glycolysis, PPP, and the electron transport chain, highlighting the interconnectivity of central carbon metabolism. Our systematic approach demonstrated the possibility of utilizing comprehensive and untargeted metabolomics to map gene-metabolite associations and decipher potential metabolic interlinks.

Source: Journal of the American Society for Mass Spectrometry

DOI: 10.1021/jasms.5c00454

Authors: Xinru Pang, Li Chen, Huan Zhang, Shiqi Zhang, Jiangjiang Zhu

Institution: The Ohio State University

Language: English

Topic: Microbial Metabolic Engineering and Bioproduction

Subfield: Molecular Biology

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

SDG: Good health and well-being

Open Access status: hybrid

Estimated APC paid: $4,500