Genome of alkaliphilic Bacillus pseudofirmus OF4 reveals adaptations that support the ability to grow in an external pH range from 7.5 to 11.4

Abstract

Summary Bacillus pseudofirmus OF4 is an extreme but facultative alkaliphile that grows non-fermentatively in a pH range from 7.5 to above 11.4 and can withstand large sudden increases in external pH. It is a model organism for studies of bioenergetics at high pH, at which energy demands are higher than at neutral pH because both cytoplasmic pH homeostasis and ATP synthesis require more energy. The alkaliphile also tolerates a cytoplasmic pH > 9.0 at external pH values at which the pH homeostasis capacity is exceeded, and manages other stresses that are exacerbated at alkaline pH, e.g. sodium, oxidative and cell wall stresses. The genome of B. pseudofirmus OF4 includes two plasmids that are lost from some mutants without viability loss. The plasmids may provide a reservoir of mobile elements that promote adaptive chromosomal rearrangements under particular environmental conditions. The genome also reveals a more acidic pI profile for proteins exposed on the outer surface than found in neutralophiles. A large array of transporters and regulatory genes are predicted to protect the alkaliphile from its overlapping stresses. In addition, unanticipated metabolic versatility was observed, which could ensure requisite energy for alkaliphily under diverse conditions.

Cardiolipin Is Dispensable for Oxidative Phosphorylation and Non-fermentative Growth of Alkaliphilic Bacillus pseudofirmus OF4

“…proposed that unusual features of the CL head group could enable a cluster of such head groups to pick up protons and then serve as a rapid and direct conduit of protons from proton pumping respiratory chain complexes to the ATP synthase. If this is a key mechanism, mutational loss of the three Cls enzymes identified in the B. pseudofirmus OF4 genome (39) would be expected to have a major negative impact on OXPHOS capacity at high pH. Study of the individual and collective roles of the Cls enzymes is also of general interest to explore in an alkaliphile that grows well, both fermentatively and non-fermentatively, in a pH range from 7.5 to Ͼ11.2.…”

The c-ring stoichiometry of ATP synthase is adapted to cell physiological requirements of alkaliphilic Bacillus pseudofirmus OF4

“…The effective pmf at the membrane surface may be larger than the bulk pmf (14-16), thus partially addressing the energetic challenge. However, alkaliphilic bacteria have also developed several adaptation strategies, which in combination support robust growth at high pH (12,13,17,18). These adaptations include alkaliphile-specific features of the ATP synthase, including changes at the c-ring's ion-binding site (19) as well as its size and stoichiometry (19)(20)(21).…”

Roles of AtpI and Two YidC-Type Proteins from Alkaliphilic Bacillus pseudofirmus OF4 in ATP Synthase Assembly and Nonfermentative Growth

“…Magnesium acquisition is a process that would be expected to be a special challenge at high pH, at which bioavailability is low, but B. pseudofirmus OF4 is apparently well adapted for that challenge. Some of those adaptations may be responsible for the need to add features to ensure adequate magnesium acquisition at more conventional pH values in this extremophile (27,51).…”

“…In the current study, we examined the effects of deletion of atpI, atpZ, or the yidC-like genes of alkaliphilic B. pseudofirmus OF4, yqjG and spoIIIJ (27). This alkaliphile produces an unusually stable c-ring that has adaptations that foster this stability and enable the enzyme to carry out proton-coupled ATP synthesis over a pH range from near neutral to higher than pH 11 (6,(28)(29)(30)(31).…”

“…were identified in the recently completed genome sequence, with locus tags of BpOF4_11410 and BpOF4_07940 (27). They were designated yqjG and spoIIIJ, respectively, as in B. subtilis (22).…”