title: Acid-adapted strains of Escherichia coli K-12 obtained by experimental evolution.
abstract: Enteric bacteria encounter a wide range of pHs throughout the human intestinal tract. We conducted experimental evolution of Escherichia coli K-12 to isolate clones with increased fitness during growth under acidic conditions (pH 4.5 to 4.8). Twenty-four independent populations of E. coli K-12 W3110 were evolved in LBK medium (10 g/liter tryptone, 5 g/liter yeast extract, 7.45 g/liter KCl) buffered with homopiperazine-N,N'-bis-2-(ethanosulfonic acid) and malate at pH 4.8. At generation 730, the pH was decreased to 4.6 with HCl. By 2,000 generations, all populations had achieved higher endpoint growth than the ancestor at pH 4.6 but not at pH 7.0. All evolving populations showed a progressive loss of activity of lysine decarboxylase (CadA), a major acid stress enzyme. This finding suggests a surprising association between acid adaptation and moderation of an acid stress response. At generation 2,000, eight clones were isolated from four populations, and their genomes were sequenced. Each clone showed between three and eight missense mutations, including one in a subunit of the RNA polymerase holoenzyme (rpoB, rpoC, or rpoD). Missense mutations were found in adiY, the activator of the acid-inducible arginine decarboxylase (adiA), and in gcvP (glycine decarboxylase), a possible acid stress component. For tests of fitness relative to that of the ancestor, lacZ::kan was transduced into each strain. All acid-evolved clones showed a high fitness advantage at pH 4.6. With the cytoplasmic pH depressed by benzoate (at external pH 6.5), acid-evolved clones showed decreased fitness; thus, there was no adaptation to cytoplasmic pH depression. At pH 9.0, acid-evolved clones showed no fitness advantage. Thus, our acid-evolved clones showed a fitness increase specific to low external pH.
authors.affiliation: Department of Biology, Kenyon College, Gambier, Ohio, USA.
authors.forename: Mark M
authors.initials: MM
authors.lastname: Harden
authors.affiliation: Department of Biology, Kenyon College, Gambier, Ohio, USA.
authors.forename: Amanda
authors.initials: A
authors.lastname: He
authors.affiliation: Department of Biology, Kenyon College, Gambier, Ohio, USA.
authors.forename: Kaitlin
authors.initials: K
authors.lastname: Creamer
authors.affiliation: Department of Biology, Kenyon College, Gambier, Ohio, USA.
authors.forename: Michelle W
authors.initials: MW
authors.lastname: Clark
authors.affiliation: Department of Biology, Kenyon College, Gambier, Ohio, USA.
authors.forename: Issam
authors.initials: I
authors.lastname: Hamdallah
authors.affiliation: Department of Biology, Kenyon College, Gambier, Ohio, USA.
authors.forename: Keith A
authors.initials: KA
authors.lastname: Martinez
authors.affiliation: Department of Biology, Kenyon College, Gambier, Ohio, USA.
authors.forename: Robert L
authors.initials: RL
authors.lastname: Kresslein
authors.affiliation: Department of Biology, Kenyon College, Gambier, Ohio, USA.
authors.forename: Sean P
authors.initials: SP
authors.lastname: Bush
authors.affiliation: Department of Biology, Kenyon College, Gambier, Ohio, USA slonczewski@kenyon.edu.
authors.forename: Joan L
authors.initials: JL
authors.lastname: Slonczewski
mesh_terms: D000143:Acids / Q000633:toxicity*; D000220:Adaptation, Biological; D003470:Culture Media / Q000737:chemistry; D024881:Drug Resistance, Bacterial; D048168:Escherichia coli K12 / Q000187:drug effects*; D029968:Escherichia coli Proteins / Q000235:genetics / Q000378:metabolism; D006863:Hydrogen-Ion Concentration; D020125:Mutation, Missense
chemical_list: D000143:Acids; D003470:Culture Media; D029968:Escherichia coli Proteins