Table 1.

Factors involved in the survival of acidic pH.

Factors involved	Mechanisms	Reference
Urease dependent mechanisms
Urease	Breakdown of urea and production of ammonia that neutralizes the acidity.	17, 42
NixA and NikR	Regulates the availability of nickel molecules for full action of metallo-enzyme, urease.	27, 28, 30, 31, 33–36
UreI	Mediates entry of urea after exposure of bacterial cell to the high acidic pH.	38–39
Arginase	Production of endogenous urea that is hydrolyzed by urease.	41
glutamine synthetase (GS), glutamate dehydrogenase (GDH), glutaminase (Ggt) and asparaginase (AsnB)	Mediates the metabolism and assimilation of NH4+ generated by periplasmic alpha-carbonic anhydrase.	43
Alpha-carbonic anhydrase	Conversion of CO2 to HCO3− and maintenance of periplasmic pH close to 6.1.	45
ExbD	Transfers energy to the outer membrane for active transportation of urea and other essential molecules at acidic pH.	48–50
ArsR and ArsS	Regulation, expression of urease gene cluster and recruitment of urease.	51, 52
Urease independent mechanism
Gastric mucus layer	Gel-like viscoelastic property of mucus facilitates movement of bacteria at acidic pH.	54
Helical bacterial shape	Provides corkscrew like movement that facilitates penetration into mucus layer	58, 60
Flagella	Acid activates the flagellar protein and movement.	65, 66
Chemotaxis and chemo-receptor	Chemoreceptor TlpB senses the environmental pH for chemotaxis	78–80
Recombinational repair proteins; RecA, RecN, RecO, RecR, Hup and PriA	Mediates recombinational repair of DNA damage caused by acid stress.	83, 91, 94, 98, 101
DNA binding protein, HP0119	Histone like hypothetical protein HP0119 physically protects the bacteria at acidic pH	105
AmiE, AmiF and aspartase	Urease independent ammonia production that neutralizes acidic pH	110–113
AtoS and CrdS	Senses acid pH and regulates expression of acid responsive genes.	117–120
Fur	Mediates iron uptake and regulates expression of acid responsive genes.	65, 121, 122, 129