A systems biology approach to investigate the effect of pH-induced gene regulation on solvent production by Clostridium acetobutylicum in continuous culture

Abstract

BackgroundClostridium acetobutylicum is an anaerobic bacterium which is known for its solvent-producing capabilities, namely regarding the bulk chemicals acetone and butanol, the latter being a highly efficient biofuel. For butanol production by C. acetobutylicum to be optimized and exploited on an industrial scale, the effect of pH-induced gene regulation on solvent production by C. acetobutylicum in continuous culture must be understood as fully as possible.ResultsWe present an ordinary differential equation model combining the metabolic network governing solvent production with regulation at the genetic level of the enzymes required for this process. Parameterizing the model with experimental data from continuous culture, we demonstrate the influence of pH upon fermentation products: at high pH (pH 5.7) acids are the dominant product while at low pH (pH 4.5) this switches to solvents. Through steady-state analyses of the model we focus our investigations on how alteration in gene expression of C. acetobutylicum could be exploited to increase butanol yield in a continuous culture fermentation.ConclusionsIncorporating gene regulation into the model of solvent production by C. acetobutylicum enables an accurate representation of the pH-induced switch to solvent production to be obtained and theoretical investigations of possible synthetic-biology approaches to be pursued. Steady-state analyses suggest that, to increase butanol yield, alterations in the expression of single solvent-associated genes are insufficient; a more complex approach targeting two or more genes is required.

Coenzyme A-transferase-independent butyrate re-assimilation in Clostridium acetobutylicum—evidence from a mathematical model

“…7 in Millat et al (2013b)). Consequently, a mathematical model assuming an alternative re-assimilation of butyrate and a pH-dependent reduced acetate formation rate, but no CtfA/B-mediated acid re-assimilation, could explain the observations reported in Haus et al (2011) andMillat et al (2013b).…”

“…and theoretical investigations (Haus et al 2011;Millat et al 2013b) indicate that the pH-induced metabolic shift under our experimental conditions is linked to a rearrangement of transcriptomic, proteomic, and metabolomic composition of the cells. Following our approach demonstrated in Millat et al (2013b), these experimental findings correspond to an acidogenic and a solventogenic phenotype which are prevalently present either at acidogenic (pH above 5.2) or solventogenic conditions (pH below 5.1) (Millat et al 2013a).…”

“…A first kinetic simulation model, to describe the dynamics of ABE fermentation in the related Clostridium saccharoperbutylacetonicum 1-4 during growth in batch culture under condition of glucose depletion, was presented in (Shinto et al 2007). A first model of the pH-induced metabolic shift in C. acetobutylicum in phosphate-limited continuous culture, was published by Haus et al (2011), which took into account an adaptation of gene expression and proteome composition to the changing external pH. Additionally, the effect of several single mutations on the product formation at acidogenic and solventogenic steady state was investigated.…”

“…In the solvent-forming wild type (Haus et al 2011;Millat et al 2013b), acetone formation is responsible for approximately 22% of all measured fermentation products, whereas it represents only 3% during acidogenesis (Millat et al 2013a). Thus, changes in response to the blockade of acetone formation should be more apparent under solventogenic conditions.…”

The putative influence of the agr operon upon survival mechanisms used by Clostridium acetobutylicum

“…In a similar vein, models of sporulation in Gram-positive bacteria predominantly concern B. subtilis, with three in particular incorporating genetic regulation of the initiation network [9,20,21] using methods similar to those that we shall exploit here. Mathematical modelling of C. acetobutylicum has concentrated on the metabolic interactions involved in the fermentation process and have successfully represented the cells either during acidogenesis or in solventogenesis [22,23,24,25,26]. However, the nature of the existing models means that the switch between the two phases has to be imposed either by an artificial switch, or by an alteration in the parameter set.…”