Shotgun proteome analysis of the bacterium Clostridium cellulolyticum

Biofuel production from lignocellulosic waste and residues is a promising option to mitigate the environmental costs associated to energy production. However, the difficulty to cost-effectively overcome lignocellulose recalcitrance hampers a widespread application of such bioprocesses. Through an integrated approach, we focused on the factors affecting cellulose reactivity and their impact on downstream fermentation. Three cellulosic manufactured materials were characterized in details: facial tissue, Whatman paper, cotton pads. The model mesophilic cellulolytic bacterium Clostridium cellulolyticum was used to study colonization and metabolic patterns during fermentation of these materials. Facial tissue was extensively colonized and exhibited the fastest degradation and the highest ethanol-to-acetate ratio. Comparing facial tissue fermentation to Whatman paper fermentation by label-free quantitative shotgun proteomics and statistical analyses, 187 proteins showed a different behavior; higher concentration levels were detected for many enzymes from the carbohydrate central metabolic pathway; distinct patterns of expression levels were observed for carbohydratases degrading cellulose and hemicellulose. Overall, lower degrees of polymerization, lower crystallinity index, and the presence of hemicelluloses could explain the higher biological reactivity and bioethanol production yields.