Functional Systems
AADB organizes genes into functional systems involved in pH homeostasis and stress response. These systems work collectively to maintain cellular pH balance and enable survival under extreme pH conditions (both acidic and alkaline). The following sections provide detailed descriptions of each functional system, their molecular mechanisms, and their roles in pH stress resistance.
The glutamate decarboxylase (GAD) system consumes protons through glutamate decarboxylation coupled to amino acid/amine exchange. This system is critical for survival in strongly acidic environments (pH ~2–3) by consuming cytosolic protons and exporting them via the GadC antiporter.
Antiporter systems regulate proton flux via cation/H+ exchange. These membrane transporters exchange ions (Na+, K+) for protons to maintain pH homeostasis, protecting cells from acid stress by exporting excess protons and scavenging protons under alkaline conditions.
Acid-activated chaperones stabilize periplasmic proteins under low pH. HdeA and HdeB chaperones are inactive at neutral pH but become activated by acid-induced structural changes, binding and stabilizing unfolded periplasmic proteins to prevent aggregation under extremely acidic conditions (pH 2–3).
Alkaline-resistance modules support cytoplasmic pH maintenance at high external pH. Bacteria use multiple strategies including Na+/H+ antiporters, cell envelope modifications, and sodium-motive force to maintain cytoplasmic pH. Alkaliphiles can maintain a cytoplasmic pH 2–2.3 units lower than external pH, enabling survival up to pH 10–11.
pH-response regulatory programs include two-component signaling and pH-linked transcriptional control. Bacteria sense pH changes through two-component systems and pH-specific regulators (e.g. CadC, EvgS/EvgA) that trigger adaptive gene expression. Global regulators like RpoS coordinate pH homeostasis responses.
General stress response modules provide cross-protection under pH extremes. The RpoS regulon orchestrates broader stress responses including DNA repair, molecular chaperones, and proteases. This system provides cross-protection and helps cells survive pH extremes.
Periplasmic pH regulation systems include urease-linked buffering in host-associated niches. Some pathogens modulate periplasmic pH as a buffer zone. Helicobacter pylori uses urease to hydrolyze urea into ammonia and CO2, creating a buffered microenvironment (pH ~6) even when external pH is ~1–2.
Membrane pH transport components include primary/secondary transport processes affecting intracellular pH. Primary proton pumps like F1F0-ATPase directly move protons to control intracellular pH. Under acid stress, ATPase can reverse operation to actively expel H+ from the cytoplasm.
Glutaminase-dependent buffering routes generate ammonia and can couple to decarboxylation-based resistance. This system utilizes L-glutamine through acid-activated glutaminase (YbaS/GlsA) to produce ammonia and glutamate. The ammonia consumes protons while glutamate feeds into the GAD pathway, extending acid resistance to pH ~2.5.
Urease-mediated neutralization buffers extreme acidity via ammonia production. Urease hydrolyzes urea into ammonia, which neutralizes acid and increases local pH. Helicobacter pylori uses this system to maintain periplasmic pH ~6 even when external pH is ~1–2, enabling gastric colonization.
Other curated pH-related mechanisms are retained for coverage and hypothesis generation. Additional mechanisms include alternative amino acid decarboxylase systems (arginine, lysine, ornithine), the arginine deiminase (ADI) pathway, and various metabolic strategies that provide secondary pH protection across different niches.
These systems are not mutually exclusive; many organisms employ multiple mechanisms simultaneously to achieve robust pH stress resistance. The integration of these functional systems enables microbial survival across a wide pH spectrum, from highly acidic (pH ~2) to highly alkaline (pH ~11) environments.