Abstract
Clostridium phytofermentans was isolated from forest soil and is distinguished by its capacity
to directly ferment plant cell wall polysaccharides into ethanol as the primary product,
suggesting that it possesses unusual catabolic pathways. The objective of the present
study was to understand the molecular mechanisms of biomass conversion to ethanol in a
single organism, Clostridium phytofermentans, by analyzing its complete genome and transcriptome
during growth on plant carbohydrates. The saccharolytic versatility of C. phytofermentans
is reflected in a diversity of genes encoding ATP-binding cassette sugar
transporters and glycoside hydrolases, many of which may have been acquired through
horizontal gene transfer. These genes are frequently organized as operons that may be
controlled individually by the many transcriptional regulators identified in the genome. Preferential
ethanol production may be due to high levels of expression of multiple ethanol dehydrogenases
and additional pathways maximizing ethanol yield. The genome also encodes
three different proteinaceous bacterial microcompartments with the capacity to compartmentalize
pathways that divert fermentation intermediates to various products. These characteristics
make C. phytofermentans an attractive resource for improving the efficiency and
speed of biomass conversion to biofuels.