title: Acid Evolution of Escherichia coli K-12 Eliminates Amino Acid Decarboxylases and Reregulates Catabolism.
abstract: Acid-adapted strains ofEscherichia coliK-12 W3110 were obtained by serial culture in medium buffered at pH 4.6 (M. M. Harden, A. He, K. Creamer, M. W. Clark, I. Hamdallah, K. A. Martinez, R. L. Kresslein, S. P. Bush, and J. L. Slonczewski, Appl Environ Microbiol 81:1932-1941, 2015, https://doi.org/10.1128/AEM.03494-14). 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 IS5insertion or IS-mediated deletion incadC, while population B11 had a point mutation affecting the arginine activatoradiYThecadCandadiYmutants failed to neutralize acid in the presence of exogenous lysine or arginine. In strain B11-1, reversion of anrpoC(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 (gamma-aminobutyric acid) and failed to survive extreme acid. Transcriptome sequencing (RNA-seq) of strain B11-1 showed upregulated genes for catabolism of diverse substrates but downregulated acid stress genes (the biofilm regulatorariR,yhiM, and Gad). Other strains showed downregulation of H2consumption mediated by hydrogenases (hyaandhyb) which release acid. Strains F9-2 and F9-3 had a deletion offnrand showed downregulation of FNR-dependent genes (dmsABC,frdABCD,hybABO,nikABCDE, andnrfAC). Overall, strains that had evolved in buffered acid showed loss or downregulation of systems that neutralize unbuffered acid and showed altered regulation of catabolism.IMPORTANCEExperimental 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.
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: Stephanie R
authors.initials: SR
authors.lastname: Penix
authors.affiliation: Department of Biology, Kenyon College, Gambier, Ohio, USA.
authors.forename: Preston J
authors.initials: PJ
authors.lastname: Basting
authors.affiliation: Department of Biology, Kenyon College, Gambier, Ohio, USA.
authors.forename: Jessie M
authors.initials: JM
authors.lastname: Griffith
authors.affiliation: Department of Biology, Kenyon College, Gambier, Ohio, USA.
authors.forename: Kaitlin E
authors.initials: KE
authors.lastname: Creamer
authors.affiliation: Department of Biology, Kenyon College, Gambier, Ohio, USA.
authors.forename: Dominic
authors.initials: D
authors.lastname: Camperchioli
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: Alexandra S
authors.initials: AS
authors.lastname: Gonzales
authors.affiliation: Department of Biology, Kenyon College, Gambier, Ohio, USA.
authors.forename: Jorge Sebastian
authors.initials: JS
authors.lastname: Chávez Erazo
authors.affiliation: Environmental Microbiology and Food Safety Laboratory, Beltsville Agricultural Research Center, U.S. Department of Agriculture, Beltsville, Maryland, USA.
authors.forename: Nadja S
authors.initials: NS
authors.lastname: George
authors.affiliation: Environmental Microbiology and Food Safety Laboratory, Beltsville Agricultural Research Center, U.S. Department of Agriculture, Beltsville, Maryland, USA.
authors.forename: Arvind A
authors.initials: AA
authors.lastname: Bhagwat
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 / Q000378:metabolism*; D001142:Aromatic-L-Amino-Acid Decarboxylases / Q000172:deficiency* / Q000235:genetics; D005075:Biological Evolution; D048168:Escherichia coli K12 / Q000201:enzymology* / Q000235:genetics / Q000378:metabolism; D029968:Escherichia coli Proteins / Q000235:genetics / Q000378:metabolism*; D015964:Gene Expression Regulation, Bacterial; D006863:Hydrogen-Ion Concentration
chemical_list: D000143:Acids; D029968:Escherichia coli Proteins; D001142:Aromatic-L-Amino-Acid Decarboxylases
keywords: Escherichia coli; GABA; RNA polymerase; acid; decarboxylase; experimental evolution; fnr; low pH