Reprogramming of Escherichia coli K-12 metabolism during the initial phase of transition from an anaerobic to a micro-aerobic environment

• Published in: PloS one Vol. 6; no. 9; p. e25501
• Main Authors: Trotter, Eleanor W, Rolfe, Matthew D, Hounslow, Andrea M, Craven, C Jeremy, Williamson, Michael P, Sanguinetti, Guido, Poole, Robert K, Green, Jeffrey
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 27.09.2011; Public Library of Science (PLoS)
• Subjects: Adaptation; Adaptation, Physiological - drug effects; Adaptation, Physiological - genetics; Aerobic conditions; Aerobiosis; Anaerobic conditions; Anaerobiosis; Analysis; Bacteria; Biology; Bioreactors; Biotechnology; Culture Techniques; Cytochrome; Deactivation; Dehydrogenases; E coli; Energy; Environment; Escherichia coli; Escherichia coli K12 - drug effects; Escherichia coli K12 - genetics; Escherichia coli K12 - growth & development; Escherichia coli K12 - metabolism; Escherichia coli Proteins - metabolism; Excretion; Fermentation; Fermentation - drug effects; Fermentation - genetics; Gene expression; Glucose; Inactivation; Iron-Sulfur Proteins - metabolism; Kinases; Medicine; Metabolism; Metabolites; Metabolome - drug effects; Metabolome - genetics; Molecular biology; Nitrates; Oxidation; Oxygen - pharmacology; Phase transitions; Phosphorylation; Physiological aspects; Proteins; Pyruvate dehydrogenase (lipoamide); Pyruvic acid; Pyruvic Acid - metabolism; Regulators; Repressor Proteins - metabolism; Respiration; RNA, Messenger - genetics; RNA, Messenger - metabolism; State space models; Time Factors; Transcription; Transcription factors; Transcriptome
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0025501

Many bacteria undergo transitions between environments with differing O₂ availabilities as part of their natural lifestyles and during biotechnological processes. However, the dynamics of adaptation when bacteria experience changes in O₂ availability are understudied. The model bacterium and facultative anaerobe Escherichia coli K-12 provides an ideal system for exploring this process. Time-resolved transcript profiles of E. coli K-12 during the initial phase of transition from anaerobic to micro-aerobic conditions revealed a reprogramming of gene expression consistent with a switch from fermentative to respiratory metabolism. The changes in transcript abundance were matched by changes in the abundances of selected central metabolic proteins. A probabilistic state space model was used to infer the activities of two key regulators, FNR (O₂ sensing) and PdhR (pyruvate sensing). The model implied that both regulators were rapidly inactivated during the transition from an anaerobic to a micro-aerobic environment. Analysis of the external metabolome and protein levels suggested that the cultures transit through different physiological states during the process of adaptation, characterized by the rapid inactivation of pyruvate formate-lyase (PFL), a slower induction of pyruvate dehydrogenase complex (PDHC) activity and transient excretion of pyruvate, consistent with the predicted inactivation of PdhR and FNR. Perturbation of anaerobic steady-state cultures by introduction of a limited supply of O₂ combined with time-resolved transcript, protein and metabolite profiling, and probabilistic modeling has revealed that pyruvate (sensed by PdhR) is a key metabolic signal in coordinating the reprogramming of E. coli K-12 gene expression by working alongside the O₂ sensor FNR during transition from anaerobic to micro-aerobic conditions.