Fig. 3.

RNA-Seq comparison of wild-type C. acetobutylicum and Δpks. STRING network analysis of genes predicted to be transcriptionally downregulated (left) and upregulated (right) by RNA-Seq in Δpks fermentation culture relative to wild type. Nodes represent differentially expressed genes, and lines represent predicted connections between genes including shared functional pathways of encoded proteins, chromosomal proximity, co-occurrence of genes in other organisms, co-expression of genes, and protein homology. For clarity, only genes with at least one predicted connection are shown. Four major concentrations of connected nodes were observed for each group (indicated by a–h), signifying the cellular pathways most affected by deletion of the pks gene. Detailed results from the RNA-Seq analysis are presented in Supplementary Data 1