pH growth preference

Edge evidence

• environmental pH regulates pH growth preference RO:0002211

  Environmental pH determines which pH conditions support growth.

  • DOI:10.1038/nrmicro2549 tolerate or grow at external pH values Review frames pH growth as a response to external pH outside the cytoplasmic range.
• acidic external pH challenges cytoplasmic pH homeostasis METPO:2007406

  Acidic environments impose inward proton stress that must be managed for growth.

  • DOI:10.1038/nrmicro2549 acid challenge conditions include increased expression and activity Supports active mechanisms under acid challenge.
• alkaline external pH challenges cytoplasmic pH homeostasis METPO:2007406

  Alkaline environments require active proton accumulation or generation to maintain cytoplasmic pH.

  • DOI:10.1038/nrmicro2549 active proton accumulation or generation in the cytoplasm Supports alkaline-pH homeostasis as a growth-enabling process.
• pH sensing regulates cytoplasmic pH homeostasis RO:0002211

  pH-sensing and signalling systems regulate homeostasis responses to acid or alkali.

  • DOI:10.1038/nrmicro2549 pH-sensing and signalling capabilities Supports regulatory sensing as part of homeostasis.
• cytoplasmic pH homeostasis enables pH growth preference RO:0002327

  Growth at preferred pH depends on maintaining intracellular pH compatible with cellular processes.

  • DOI:10.1038/nrmicro2549 robust mechanisms for cytoplasmic pH homeostasis Supports cytoplasmic pH homeostasis as central to growth under pH stress.
• proton-translocating F1F0-ATPase contributes to cytoplasmic pH homeostasis RO:0002326

  The proton-translocating F1F0-ATPase mediates pH homeostasis supporting growth under low pH.

  • DOI:10.1093/femsre/fuad062 pH homeostasis mediated by the proton-translocating F1F0-ATPase; general across taxa.
• acidic external pH induces amino-acid decarboxylase systems

  Low external pH induces amino-acid decarboxylase systems that consume protons.

  • DOI:10.1093/femsre/fuad062 amino-acid decarboxylase systems (GAD, agmatine/arginine decarboxylation) that consume protons and raise cytoplasmic alkalinity.
• amino-acid decarboxylase systems enables amino-acid decarboxylation RO:0002327

  Decarboxylase systems carry out amino-acid decarboxylation.

  • DOI:10.1093/femsre/fuad062 amino-acid decarboxylase systems that consume protons and raise cytoplasmic alkalinity.
• amino-acid decarboxylation contributes to cytoplasmic pH homeostasis RO:0002326

  Amino-acid decarboxylation consumes protons and raises cytoplasmic alkalinity, aiding pH homeostasis.

  • DOI:10.1093/femsre/fuad062 consume protons and raise cytoplasmic alkalinity.
• Na+/H+ antiport contributes to cytoplasmic pH homeostasis RO:0002326

  Na+/H+ antiport (notably the Mrp system) is the major mechanism for alkaline pH homeostasis.

  • DOI:10.1038/nrmicro2549 Na+/H+ antiporters (notably the multicomponent Mrp system) are the major mechanism for alkaliphile pH homeostasis.
• proton-consuming reaction genes associated with acidic external pH biolink:associated_with

  Genes for proton-consuming reactions (decarboxylases/deaminases) are consistently associated with lower pH preference.

  • DOI:10.1126/sciadv.adf8998 proton-consuming reactions (decarboxylases, deaminases) consistently associated with pH preference across environments.
• Na+/H+ antiporter genes associated with alkaline external pH biolink:associated_with

  Na+/H+ antiporter genes (PhaGF/MnhG/MrpF/YufB) are associated with higher pH preference.

  • DOI:10.1126/sciadv.adf8998 Na+/H+ antiporters PhaGF, MnhG, MrpF, YufB associated with higher pH preference.