S31: Genome-wide Transcriptomic Analyses of Clostridium beijerinckii NCIMB 8052 during Transition from Acidogenesis to Solventogenesis using High-throughput RNA-Seq Technology

Clostridium beijerinckii is an important solvent producing microorganism. The genome of C. beijerinckii NCIMB 8052 has recently been sequenced. However, the transcriptome configuration and genome-wide transcription are still not well understood. In this study, we conducted a single-nucleotide resolution analysis of the C. beijerinckii NCIMB 8052 transcriptome using high-throughput RNA-Seq technology. We identified the transcription start sites and operon structure throughout the genome. We confirmed the structure of important gene operons involved in metabolic pathways for acid and solvent production in C. beijerinckii 8052, including pta-ack, ptb-buk, hbd-etfA-etfB-crt (bcs) and ald-ctfA-ctfB-adc (sol) operons; we defined important operons related to chemotaxis/motility, transcriptional regulation, stress response, fatty acids biosynthesis, etc. Furthermore, based on normalized quantification of gene expression, genome-wide dynamic transcriptional program during shift from acidogenesis to solventogenesis was investigated. The onset of solventogenesis in C. beijerinckii 8052 was concurrent with the initiation of sporulation. The expression of primary metabolic genes (acid formation, solventogenesis, sporulation, chemotaxis/motility and etc.) all demonstrated temporal patterns in concert with the shift from acidogenesis to solventogenesis. Novel expression patterns of other functional gene classes were also identified, including heat shock, amino acid biosynthesis, inorganic ions transporter genes, etc. Besides, we identified 78 silent genes and 177 putative housekeeping genes based on normalized transcription measurement. We also observed that more than 30% of pseudogenes had significant transcriptional activities during fermentation. Genome-wide transcriptomic analysis provided important supplemental information on the accuracy of annotation of the C. beijerinckii genome, and revealed additional gene functions and regulation in C. beijerinckii.