Journal Article

Redox controls metabolic robustness in the gas-fermenting acetogen Clostridium autoethanogenum

Köpke, Michael, Nielsen, Lars Keld, Simpson, Séan Dennis, Tappel, Ryan, de Souza Pinto Lemgruber, Renato, Valgepea, Kaspar, Plan, Manuel, Mahamkali, Vishnuvardhan, Marcellin, Esteban

2020

Overview

Living biological systems display a fascinating ability to self-organize their metabolism. This ability ultimately determines the metabolic robustness that is fundamental to controlling cellular behavior. However, fluctuations in metabolism can affect cellular homeostasis through transient oscillations. For example, yeast cultures exhibit rhythmic oscillatory behavior in high cell-density continuous cultures. Oscillatory behavior provides a unique opportunity for quantitating the robustness of metabolism, as cells respond to changes by inherently compromising metabolic efficiency. Here, we quantify the limits of metabolic robustness in self-oscillating autotrophic continuous cultures of the gas-fermenting acetogen Clostridium autoethanogenum. Online gas analysis and high-resolution temporal metabolomics showed oscillations in gas uptake rates and extracellular byproducts synchronized with biomass levels. The data show initial growth on CO, followed by growth on CO and H₂. Growth on CO and H₂ results in an accelerated growth phase, after which a downcycle is observed in synchrony with a loss in H₂ uptake. Intriguingly, oscillations are not linked to translational control, as no differences were observed in protein expression during oscillations. Intracellular metabolomics analysis revealed decreasing levels of redox ratios in synchrony with the cycles. We then developed a thermodynamic metabolic flux analysis model to investigate whether regulation in acetogens is controlled at the thermodynamic level. We used endo- and exo-metabolomics data to show that the thermodynamic driving force of critical reactions collapsed as H₂ uptake is lost. The oscillations are coordinated with redox. The data indicate that metabolic oscillations in acetogen gas fermentation are controlled at the thermodynamic level.

• Publisher: National Academy of Sciences
• Subject: Biological Sciences / Carbon monoxide / Cell density / Clostridium / Fermentation / Gas analysis / Homeostasis / Metabolic flux / Metabolism / Metabolomics / Oscillations / Rhythms / Robust control / Robustness / Systems Biology / Transient oscillations / Yeast