Acid evolution deletes amino-acid decarboxylases and reregulates catabolism of Escherichia coli K-12

Acid-adapted strains of Escherichia coli K-12 W3110 evolved in media buffered at pH 4.6. Revised genomic analysis of these strains using breseq revealed IS-driven insertions and deletions that knocked out regulators CadC (acid induction of lysine decarboxylase), GadX (acid induction of glutamate decarboxylase), and FNR (anaerobic regulator). Each acid-evolved strain showed loss of one or more amino acid decarboxylase systems, which normally help neutralize external acid (from pH 5 to pH 6 or higher) and increase survival in extreme acid (pH 2). Strains from populations B11, H9, and F11 had an IS5 insertion or IS-mediated deletion in cadC, while populations B11 and H9 had point mutations affecting arginine activator adiY. The cadC and adiY mutants failed to neutralize acid in the presence of exogenous lysine or arginine. In strain B11-1, reversion of an rpoC (RNA polymerase) mutation partly restored arginine-dependent neutralization. All eight strains showed deletion or downregulation of the Gad acid-fitness island. The Gad deletion strains lost GABA production and failed to survive extreme acid (pH 2). RNA-seq of strain B11-1 showed upregulated genes for catabolism of diverse substrates, but downregulated acid-stress genes (ariR biofilm regulator, yhiM, Gad). Other strains showed downregulation of H2-consumption hydrogenases (hya and hyb). Strains F9-2, F9-3 had a deletion of fnr, and showed down-regulation of FNR-dependent genes (dmsABC, frdABCD, hybABO, nikABCDE, nrfAC). Overall, strains that had evolved in buffered acid (pH 4.6) showed loss or downregulation of systems that neutralize unbuffered acid, and altered regulation of catabolism.