Figure 3
The systems approach for YgfI transcriptional factor function prediction. (A-B) The genome-wide binding of YgfI and the zoom-in for the dhaK binding site. Transcriptomic profile for the YgfI regulated dhaK gene. (D-E) The YgfI function was assessed based on the growth phenotype under different conditions. The growth measurement of the ygfI mutant (orange line) compared to the wild type BW25113 strain of E. coli was measured in 96-well plates in M9 medium or the same medium supplemented with 7 mM l-threonine (C) or M9 medium with glycerol as the carbon source (F) The glycerol utilization pathway – glycerol kinase (GK, glpK), glycerol-3phosphate dehydrogenase (G3PDH, glpD), glycerol dehydrogenase (GlyDH, gldA), dihydroacetone kinase (DHAK, dhaKLM). RNA-seq differentially expressed genes are marked by a red arrow. Transcriptomic data analysis for the ygfI mutant compared to the wild type BW25113 strain of E. coli shows the glycerol and l-threonine utilization pathway genes (the DEGs are marked by arrows, predicted YgfI binding site marked by red stars) regulation. (G) The concentration (mM) for the formate (orange line) and acetate (blue line) produced by E. coli BW25113 WT (circles) and ygfI deletion mutant (triangles) strains in M9 glucose medium supplemented by 7 mM Thr (microaerobic conditions).
