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The Dynamic Biomass Constituting Equation for the Genome-Scale Model of the Biofuels Producer Clostridium Acetobutylicum

Ryan S. Senger, Department of Chemical Engineering, University of Delaware, Delaware Biotechnology Institute, 15 Innovation Way, Newark, DE 19711 and Eleftherios T. Papoutsakis, Dept. of Chemical Engineering, Delaware Biotechnology Institute, 15 Innovation Way, Newark, DE 19711.

It has become well-established that genome-scale models using metabolic flux analysis provide the mathematical link between a cellular genotype and its expressed phenotype. However, this is generally done by calculating the metabolic capacity or phenotypic phase plane, which consists of families of solutions. When considering cell growth in a genome-scale model, empirical relations describing the compositions of the biomass building-blocks: DNA, RNA, protein, lipids, cell wall, and solute pools are combined with energetic requirements to form the biomass constituting (or cell growth) equation. Here, we describe the dynamic nature of the biomass constituting equation necessary for predicting vegetative growth and metabolism of Clostridium acetobutylicum, an endospore forming, strict anaerobe which is the type strain for the industrial acetone, butanol, and ethanol (ABE) fermentation. The cellular maintenance energy component of the biomass constituting equation was found to be about 4-times greater in the lag and late exponential growth phases than what was calculated for the maximum rate during the vegetative growth phase. Considering that C. acetobutylicum takes on energy-intensive processes such as spore germination during the early lag phase, the initiation of sporulation events and the development of solvent tolerance mechanisms in the late exponential and early stationary growth phases, these calculations enabled modeling of the full exponential growth phase consistent with experimental data. Our method was also used to analyze and optimize the lipid component of the biomass constituting equation, a component which is well-known to change in clostridia cultures in response to the accumulation of weak acids and solvents in the extracellular environment.