Figure 5.

Mechanistic model of significantly differentially regulated genes and RAST subsystems during butyrate challenge in comparison to steady state (up-/down regulation is indicated by arrows). Regulated features common to both groups (POR+CARB) are shown on the left (a), whereas features specific for POR are displayed on the right (b). Common responses comprised a downregulation of lamB and ompF genes associated with iron uptake, whereas the general stress response, genes encoding enzymes involved in cysteine and biotin synthesis as well as those encoding specific metal transporters were upregulated. Strains of the POR group additionally increased expression of several stress response genes primarily connected to acid stress response, whereas those involved in branched-chain amino acid synthesis were downregulated. RAST subsystems are given as boxes (except for iron acquisition that represents a RAST category; acid and general stress responses are not specifically annotated in RAST and were manually categorized), single proteins are shown as circles. Effects of deprotonated butyrate (SCFA⁻), which can enter the periplasm through porins and intercalate in the inner membrane, as well as its protonated form (SCFA+H⁺), which can cause acidic stress in the periplasm by diffusion through the outer membrane subsequently releasing protons, are indicated. Cycloproprane-fatty acyl phospholipid synthase (cfa) is displayed with its main function to catalyze integration of cyclopropane ring in membrane fatty acids. The siderophore ferrichrome, FepA and CadB (standard font) are shown for completeness, despite not being significantly regulated in either group. For detailed explanation see the text and Tables S4(b, c) and S5.