2-07: Global profiling of Clostridium thermocellum transcripts required for fermenting pretreated switchgrass or populus

Clostridium thermocellum is a thermophilic, obligate anaerobic bacterium that can solubilize biomass during fermentative growth to produce ethanol and other metabolic byproducts. Relatively little is known about the transcriptional machinery it uses and may alter when growing on different biomass substrates. The C. thermocellum ATCC 27405 genome was sequenced and annotated in 2006. Recently, we used the Prodigal gene finding program to predict 3,173 candidate protein-encoding gene models for the C. thermocellum ATCC 27405 genome. The majority of genes were consistent with the previous version, but there were important differences including 89 new genes, 67 that were deleted and another 147 that were modified. To investigate what genes are important for growth on different biomasses, we cultured C. thermocellum ATCC 27405 at 58°C in duplicate controlled fermentors with either 5 g/L (dry weight basis) pretreated Switchgrass or  Populus as substrates. C. thermocellum biomass fermentation profiles were collected for 140 h and showed the cells actively produced ethanol and other metabolic byproducts until 40 h post-inoculation. Samples were collected at 12 h and 37 h for transcriptomic profiling using NimbleGen high-density DNA microarrays and Illumina-based RNA-Seq analysis. We generated approximately 100M reads for each sample, and > 99.6 % of the reads did not map to 5, 16, 23S rRNA sequences. One of the most highly expressed genes on biomass was a newly predicted gene. Differences between RNA-Seq and microarray transcript profiles and between different conditions will be discussed.