title: Cytoplasmic acidification and the benzoate transcriptome in Bacillus subtilis.
abstract: BACKGROUND
  Bacillus subtilis encounters a wide range of environmental pH. The bacteria maintain cytoplasmic pH within a narrow range. Response to acid stress is a poorly understood function of external pH and of permeant acids that conduct protons into the cytoplasm.
  
  
  RESULTS
  Cytoplasmic acidification and the benzoate transcriptome were observed in Bacillus subtilis. Cytoplasmic pH was measured with 4-s time resolution using GFPmut3b fluorimetry. Rapid external acidification (pH 7.5 to 6.0) acidified the B. subtilis cytoplasm, followed by partial recovery. Benzoate addition up to 60 mM at external pH 7 depressed cytoplasmic pH but left a transmembrane Delta pH permitting growth; this robust adaptation to benzoate exceeds that seen in E. coli. Cytoplasmic pH was depressed by 0.3 units during growth with 30 mM benzoate. The transcriptome of benzoate-adapted cells was determined by comparing 4,095 gene expression indices following growth at pH 7, +/- 30 mM benzoate. 164 ORFs showed > or = 2-fold up-regulation by benzoate (30 mM benzoate/0 mM), and 102 ORFs showed > or = 2-fold down-regulation. 42% of benzoate-dependent genes are regulated up or down, respectively, at pH 6 versus pH 7; they are candidates for cytoplasmic pH response. Acid-stress genes up-regulated by benzoate included drug resistance genes (yhbI, yhcA, yuxJ, ywoGH); an oligopeptide transporter (opp); glycine catabolism (gcvPA-PB); acetate degradation (acsA); dehydrogenases (ald, fdhD, serA, yrhEFG, yjgCD); the TCA cycle (citZ, icd, mdh, sucD); and oxidative stress (OYE-family yqjM, ohrB). Base-stress genes down-regulated by benzoate included malate metabolism (maeN), sporulation control (spo0M, spo0E), and the SigW alkali shock regulon. Cytoplasmic pH could mediate alkali-shock induction of SigW.
  
  
  CONCLUSIONS
  B. subtilis maintains partial pH homeostasis during growth, and withstands high concentrations of permeant acid stress, higher than for gram-negative neutralophile E. coli. The benzoate adaptation transcriptome substantially overlaps that of external acid, contributing to a cytoplasmic pH transcriptome.
authors.affiliation: Department of Biology, Kenyon College, Gambier, Ohio, United States of America.
authors.forename: Ryan D
authors.initials: RD
authors.lastname: Kitko
authors.forename: Rebecca L
authors.initials: RL
authors.lastname: Cleeton
authors.forename: Erin I
authors.initials: EI
authors.lastname: Armentrout
authors.forename: Grace E
authors.initials: GE
authors.lastname: Lee
authors.forename: Ken
authors.initials: K
authors.lastname: Noguchi
authors.forename: Melanie B
authors.initials: MB
authors.lastname: Berkmen
authors.forename: Brian D
authors.initials: BD
authors.lastname: Jones
authors.forename: Joan L
authors.initials: JL
authors.lastname: Slonczewski
mesh_terms: D001412:Bacillus subtilis / Q000166:cytology / Q000187:drug effects* / Q000235:genetics* / Q000254:growth & development; D001565:Benzoates / Q000494:pharmacology*; D016000:Cluster Analysis; D003593:Cytoplasm / Q000187:drug effects / Q000378:metabolism*; D015536:Down-Regulation / Q000187:drug effects; D020869:Gene Expression Profiling; D015964:Gene Expression Regulation, Bacterial / Q000187:drug effects*; D049452:Green Fluorescent Proteins / Q000378:metabolism; D006851:Hydrochloric Acid / Q000494:pharmacology*; D006863:Hydrogen-Ion Concentration / Q000187:drug effects; D009876:Operon / Q000235:genetics; D020133:Reverse Transcriptase Polymerase Chain Reaction; D013312:Stress, Physiological / Q000187:drug effects; D015854:Up-Regulation / Q000187:drug effects
chemical_list: D001565:Benzoates; D049452:Green Fluorescent Proteins; D006851:Hydrochloric Acid