Abstract
BackgroundClostridium thermocellum is a gram-positive thermophile that can directly convert lignocellulosic material into biofuels. The metabolism of C. thermocellum contains many branches and redundancies which limit biofuel production, and typical genetic techniques are time-consuming. Further, the genome sequence of a genetically tractable strain C. thermocellum DSM 1313 has been recently sequenced and annotated. Therefore, developing a comprehensive, predictive, genome-scale metabolic model of DSM 1313 is desired for elucidating its complex phenotypes and facilitating model-guided metabolic engineering.ResultsWe constructed a genome-scale metabolic model iAT601 for DSM 1313 using the KEGG database as a scaffold and an extensive literature review and bioinformatic analysis for model refinement. Next, we used several sets of experimental data to train the model, e.g., estimation of the ATP requirement for growth-associated maintenance (13.5 mmol ATP/g DCW/h) and cellulosome synthesis (57 mmol ATP/g cellulosome/h). Using our tuned model, we investigated the effect of cellodextrin lengths on cell yields, and could predict in silico experimentally observed differences in cell yield based on which cellodextrin species is assimilated. We further employed our tuned model to analyze the experimentally observed differences in fermentation profiles (i.e., the ethanol to acetate ratio) between cellobiose- and cellulose-grown cultures and infer regulatory mechanisms to explain the phenotypic differences. Finally, we used the model to design over 250 genetic modification strategies with the potential to optimize ethanol production, 6155 for hydrogen production, and 28 for isobutanol production.ConclusionsOur developed genome-scale model iAT601 is capable of accurately predicting complex cellular phenotypes under a variety of conditions and serves as a high-quality platform for model-guided strain design and metabolic engineering to produce industrial biofuels and chemicals of interest.Electronic supplementary materialThe online version of this article (doi:10.1186/s13068-016-0607-x) contains supplementary material, which is available to authorized users.
Highlights
Clostridium thermocellum is a gram-positive thermophile that can directly convert lignocellulosic material into biofuels
Of particular interest for consolidated bioprocessing (CBP) is the gram-positive thermophile Clostridium thermocellum, which exhibits a high growth rate on cellulose [5, 6] and can endogenously produce the biofuels ethanol [7], hydrogen [8], and isobutanol [9]. These desirable phenotypes are feasible because C. thermocellum possesses a large, organized, extracellular cellulosome [10, 11] which is highly efficient at degrading lignocellulosic materials [12]
Model construction and comparison Following the construction process outlined in “Methods”, we obtained the C. thermocellum DSM 1313 genome-scale metabolic model (GEM), named iAT601 following convention [26, 39]. This new model presents a significant improvement from the existing ATCC 27405 GEM iSR432 [26] by incorporating very recently expanded knowledge of C. thermocellum metabolism
Summary
Clostridium thermocellum is a gram-positive thermophile that can directly convert lignocellulosic material into biofuels. Of particular interest for CBP is the gram-positive thermophile Clostridium thermocellum, which exhibits a high growth rate on cellulose [5, 6] and can endogenously produce the biofuels ethanol [7], hydrogen [8], and isobutanol [9]. These desirable phenotypes are feasible because C. thermocellum possesses a large, organized, extracellular cellulosome [10, 11] which is highly efficient at degrading lignocellulosic materials [12]. This branched metabolism, makes production of a single product such as ethanol in C. thermocellum quite challenging
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