Redox controls metabolic robustness in the gas-fermenting acetogenClostridium autoethanogenum

Abstract

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 acetogenClostridium 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 H2results in an accelerated growth phase, after which a downcycle is observed in synchrony with a loss in H2uptake. 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 H2uptake is lost. The oscillations are coordinated with redox. The data indicate that metabolic oscillations in acetogen gas fermentation are controlled at the thermodynamic level.

The Metabolism of Clostridium ljungdahlii in Phosphotransacetylase Negative Strains and Development of an Ethanologenic Strain

“…If this is the case, adhE1 regulation may not be an autotrophic mechanism per se, but rather in response to reducing gases or redox state, regardless of the presence of sugar. Alternatively, a recent study looking at C. autoethanogenum autotrophic growth suggests that ethanol formation through ADHE may be thermodynamically unfeasible under certain conditions and that AOR is important for energy generation and redox balance (Mahamkali et al, 2020). These factors could explain the lack of growth in the presence of syngas.…”

Modeling a co-culture of Clostridium autoethanogenum and Clostridium kluyveri to increase syngas conversion to medium-chain fatty-acids

“…However, the acid stress response is difficult to simulate in GEMs, which possibly results in the differences observed between the model prediction and experimental results. In addition it has been observed oscillations in gas uptake rates and extracellular byproducts synchronized with biomass levels in C. autoethanogenum [56] . This could lead to thermodynamic changes affecting the reversibility of reactions and thus, the product range.…”

Synthetic Biology on Acetogenic Bacteria for Highly Efficient Conversion of C1 Gases to Biochemicals

“…Interestingly, ethanol production was specifically increased by 1.5~1.8-fold under CO autotrophic conditions when adhE genes were deleted in C. autoethanogenum . This indicates that using the AOR route is advantageous for ethanol production rather than the AdhE pathway in C. autoethanogenum under CO conditions ( Table 2 ) [ 28 , 91 ]. Moreover, researchers expressed heat shock proteins such as GroEL, GroES, and DnaK in C. ljungdahlii or C. autoethanogenum , and its production was increased by enhancing resistance to the produced ethanol ( Table 3 ) [ 49 , 92 ].…”

“…GEMs contain the entire set of known biochemical reactions taking place in an organism and allow us to predict, in silico, the flux distribution across the metabolic pathway. Based on in silico simulation/analysis using GEMs, the carbon flux or energy balance of acetogens during C1 fixation could be better understood [ 37 , 89 , 91 , 113 , 114 , 115 , 116 , 117 ]. This large amount of information based on systems biology can help understand the genetic regulation system for the C1 fixation process of acetogens.…”