Comparative genomic and transcriptomic analysis revealed genetic characteristics related to solvent formation and xylose utilization in Clostridium acetobutylicum EA 2018

Transcriptomic profiling of gene expression in EA 2018 relative to that of ATCC824 revealed several key genes related to solvent formation. For example, spo0A and adhEII have higher expression level, and most of the acid formation related genes have lower expression level in EA 2018. Cells for RNA isolation were grown on P2 medium and collected at 9 h, 13 h, 17 h, 21 h, 24 h and 30 h by centrifugation at 4°C and 4500 x g for 10 min. Total RNA was extracted and purified by using Trizol (Invitrogen, Carlsbad, CA, USA) and RNeasy cleanup kit (Qiagen, Inc., Valencia, CA, USA) according to the manufacturer’s protocol. The total RNA yield was quantified by spectrophotometric analysis (NanoDrop Technology, Cambridge, UK) and the quality was verified by gel electrophoresis. Agilent oligonucleotide microarrays technology was used for monochromic analysis, in which probes (size: 60bp; three replicates for each ORF) from the two groups were labeled by incorporation of cyanine 3 (Cy3) (Agilent Technologies, Palo Alto, CA, USA). Average linkage hierarchical clustering was performed using Cluster 3.0, and gene clusters were visualized in Treeview