Fig. 6: The effect of ΔdatA, ΔDARS1 and ΔDARS2 deletion on the proteome of E. coli.

A Graphical representation of the genomic position of the DnaA regulon (black lines), of the dnaA gene (magenta line) and of known DnaA interaction loci (grey boxes). The number between brackets indicate the number of DnaA boxes on each gene. The white and blue line represents the count of DnaA boxes on the chromosome of E. coli MG1655, while the yellow area represents the region with significant DnaA boxes enrichment around oriC. Distances from the origin are expressed in centisomes, starting at oriC. B, C Global changes in the proteomes of (B) E. coli Δ3D in either slow (green), intermediate (blue) or fast (purple) growth regime or (C) E. coli ΔdatA, E. coli ΔDARS1 and E. coli ΔDARS2 during slow growth. In all cases, the proteomes are compared to E. coli MG1655 dnaA-PAmCherry2.1 in the same growth condition. Log₁₀ of fold changes in protein intensity are plotted against significance (-log₁₀(false discovery rate)), with cutoffs placed at 2.5 fold-change in expression and a false discovery rate of <0.05. Proteins outside the cutoffs are coloured according to the growth regime, while other proteins are in grey. Members of the DnaA regulon are circled in black, whereas DnaA is circled in magenta. D Principal component analysis showing all biological replicates for E. coli MG1655 dnaA-PAmCherry2.1 (WT), E. coli Δ3D, E. coli ΔdatA, E. coli ΔDARS1 and E. coli ΔDARS2 in all relevant growth conditions. Source data are provided as a Source Data file. The complete set of protein intensity signals is available in PRIDE.