Abstract
BackgroundThe increase in glycerol obtained as a byproduct of biodiesel has encouraged the production of new industrial products, such as 1,3-propanediol (PDO), using biotechnological transformation via bacteria like Clostridium butyricum. However, despite the increasing role of Clostridium butyricum as a bio-production platform, its metabolism remains poorly modeled.ResultsWe reconstructed iCbu641, the first genome-scale metabolic (GSM) model of a PDO producer Clostridium strain, which included 641 genes, 365 enzymes, 891 reactions, and 701 metabolites. We found an enzyme expression prediction of nearly 84% after comparison of proteomic data with flux distribution estimation using flux balance analysis (FBA). The remaining 16% corresponded to enzymes directionally coupled to growth, according to flux coupling findings (FCF). The fermentation data validation also revealed different phenotype states that depended on culture media conditions; for example, Clostridium maximizes its biomass yield per enzyme usage under glycerol limitation. By contrast, under glycerol excess conditions, Clostridium grows sub-optimally, maximizing biomass yield while minimizing both enzyme usage and ATP production. We further evaluated perturbations in the GSM model through enzyme deletions and variations in biomass composition. The GSM predictions showed no significant increase in PDO production, suggesting a robustness to perturbations in the GSM model. We used the experimental results to predict that co-fermentation was a better alternative than iCbu641 perturbations for improving PDO yields.ConclusionsThe agreement between the predicted and experimental values allows the use of the GSM model constructed for the PDO-producing Clostridium strain to propose new scenarios for PDO production, such as dynamic simulations, thereby reducing the time and costs associated with experimentation.
Highlights
The increase in glycerol obtained as a byproduct of biodiesel has encouraged the production of new industrial products, such as 1,3-propanediol (PDO), using biotechnological transformation via bacteria like Clostridium butyricum
GapFind [43] analysis of the draft model identified 303 blocked metabolites, which were reduced to 63 by adding 59 reactions based on experimental fermentation evidence from Clostridium butyricum cultured in glycerol [15, 19, 44] and on curated genome-scale metabolic (GSM) models from other solventogenic clostridia [16, 45,46,47,48,49,50,51,52]
The biomass reaction was adapted from C. beijerinckii GSM [45], which does not account for the proton formation associated with ATP hydrolysis during the growth-associated maintenance (GAM), as is observed in C. acetobutylicum [49]
Summary
The increase in glycerol obtained as a byproduct of biodiesel has encouraged the production of new industrial products, such as 1,3-propanediol (PDO), using biotechnological transformation via bacteria like Clostridium butyricum. The rising biodiesel industry has resulted in a major overproduction of glycerol as a byproduct, which threatens the economic viability of this industry [1, 2]. This situation has spurred research into glycerol utilization as a carbon source [3,4,5] and for the generation of products such as 1,3-propanediol (PDO), a precursor of Serrano-Bermúdez et al BMC Systems Biology (2017) 11:58 of up to 137% and 78%, respectively [11,12,13]. At present, metabolic models based on genome annotation information, known as genome-scale metabolic (GSM) models [17, 18], are lacking for Clostridium butyricum
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