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

Acid-adapted strains of Escherichia coli K-12 W3110 were obtained by serial culture in media buffered at pH 4.6 (Harden et al. 2015). Revised genomic analysis of these strains revealed insertion sequence (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 (pH 5 to 6) 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 population B11 had a point mutation 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. Strains with the Gad deletion lost the ability to produce GABA and failed to survive extreme acid. 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 H 2 -consumption hydrogenases ( hya and hyb ) which release acid. Strains F9-2 and 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 showed loss or downregulation of systems that neutralize unbuffered acid, and altered regulation of catabolism. IMPORTANCE Experimental evolution of an enteric bacterium under a narrow buffered range of acid pH leads to loss of genes that enhance fitness above or below the buffered pH range, including loss of enzymes that may raise external pH in the absence of buffer. Prominent modes of evolutionary change involve IS-mediated insertions and deletions that knock out key regulators. Over generations of acid stress, catabolism undergoes reregulation in ways that differ for each evolving strain.