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

Author
item HE, AMANDA - Kenyon College
item PENIX, STEPHANIE - Kenyon College
item BASTING, PRESTON - Kenyon College
item GRIFFITH, JESSIE - Kenyon College
item CREAMER, KAITLIN - Kenyon College
item CAMPERCHIOLI, DOMINIC - Kenyon College
item CLARK, MICHELLE - Kenyon College
item GONZALES, ALEXANDRA - Kenyon College
item JORGE, SEBASTIAN - Kenyon College
item George, Nadja
item Bhagwat, Arvind
item SLONCZEWSKI, JOAN - Kenyon College

Submitted to: Applied and Environmental Microbiology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/1/2017
Publication Date: 4/7/2017
Citation: He, A., Penix, S.R., Basting, P.J., Griffith, J.M., Creamer, K.E., Camperchioli, D., Clark, M.W., Gonzales, A.S., Jorge, S., George, N.S., Bhagwat, A.A., Slonczewski, J.L. 2017. Acid evolution deletes amino-acid decarboxylases and reregulates catabolism of Escherichia coli K-12. Applied and Environmental Microbiology. 83(12):1-13. https://doi.org/10.1128/AEM.00442-17.
DOI: https://doi.org/10.1128/AEM.00442-17

Interpretive Summary: Environmental stress factors that contribute to strain variations in enteric bacteria are not fully understood. Enteric microorganisms such as food-borne pathogens face gastric stomach acidity as first challenge in human stomach and there are several food surface cleansing agents which are acidic in pH. Experimental evolution under a narrow buffered range of acid pH was set up to examine genomic and phenotype changes in a model microorganism, E. coli K-12. The fitness advantage in evolved strains was observed to be due to varied ability of carbon source utilization under limited oxygen supply. Genetic changes in evolving populations were observed to be due to naturally occurring genetic insertion elements (IS). Understanding how enteric microorganisms evolve under environmental stress conditions will help us provide insights into how food-borne pathogens thrive outside host gut.

Technical Abstract: Genomic, transcriptomic and phenotypic analysis was conducted for strains of Escherichia coli K-12 W3110 evolved in media buffered at pH 4.6-4.8 (Harden et al. 2015). Revised genomic analysis 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 IS5 insertions 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 point 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 up-regulation of genes for catabolism of diverse substrates, but downregulation of some acid-stress genes (ariR biofilm regulator, Gad). Other strains showed down-regulation of H2-consumption hydrogenases (hya and hyb) (Hayes 2005; Riggins 2013; Noguchi; Trchounian). The F9-1 strain 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 acid, and altered expression of various components of catabolism.