Benzoate and Salicylate Tolerant Strains Lose Antibiotic Resistance during Laboratory Evolution of<i>Escherichia coli</i>K-12

Creamer, Kaitlin E.; Ditmars, Frederick S.; Basting, Preston J.; Kunka, Karina S; Hamdallah, Issam N; Bush, Sean P.; Scott, Zachary; He, Amanda; Penix, Stephanie R.; Gonzales, Alexandra S.; Eder, Elizabeth K.; Camperchioli, Dominic; Berndt, Adama; Clark, Michelle W.; Rouhier, Kerry A; Slonczewski, Joan L.

doi:10.1101/063271

Cited by 5 publications

(41 citation statements)

References 96 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…H9 mutations that may have affected acid survival occurred in yej, inner membrane proteins, and in the intergenic region between rhaA and rhaD, the region within the L-rhamnose degradation pathway (Table S1). Previously, we reported a similar loss of Gad during evolution in the presence of benzoic acid buffered at pH 6.5 (32). Some of the benzoate-evolved strains show loss of multidrug resistance.…”

Section: Resultsmentioning

confidence: 73%

“…The procedure for measuring GABA production via glutamate decarboxylase was modified from that of Creamer et al and Ma et al (32,48). Strains were cultured overnight in LB medium (10 g/liter tryptone, 5 g/liter yeast extract, 100 mM NaCl, 10 mM glutamine) buffered with 100 mM MES, Table S1 13 JLSE0080 H9-2 See Table S1 13 JLSE0083 B11-1 See Table S1 13 JLSE0084 B11-2 See Table S1 13 JLSE0091 F11-1 See Table S1 13 JLSE0092 F11-2 See Table S1 13 JLSE0137 F9-2 See Table S1 13 JLSE0138 F9-3 See Table S1 (49).…”

Section: Methodsmentioning

confidence: 99%

See 1 more Smart Citation

Acid Evolution of Escherichia coli K-12 Eliminates Amino Acid Decarboxylases and Reregulates Catabolism

Penix

Basting

et al. 2017

Appl Environ Microbiol

Self Cite

View full text Add to dashboard Cite

Acid-adapted strains of Escherichia coli K-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, https://doi.org/10.1128/AEM. . 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 the 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 (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 regulator ariR, yhiM, and Gad). Other strains showed downregulation of H 2 consumption mediated by hydrogenases (hya and hyb) which release acid. Strains F9-2 and F9-3 had a deletion of fnr and showed downregulation of FNR-dependent genes (dmsABC, frdABCD, hybABO, nikABCDE, and nrfAC). Overall, strains that had evolved in buffered acid showed loss or downregulation of systems that neutralize unbuffered acid and showed 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.KEYWORDS acid, Escherichia coli, experimental evolution, GABA, low pH, RNA polymerase, decarboxylase, fnr E nteric bacteria need to survive a wide range of pH values throughout the human intestinal tract. The pH of the intestinal tract ranges from 1.5 to 3.5 in the stomach, increases to 4 to 7 in the duodenum, reaches 7 to 9 in the jejunum, and decreases to pH 5 to 6 in the cecum (1). On a microscopic scale, extreme gradients of pH occur across the intestinal epithelium where enterobacteria adhere. To cope with such conditions, Escherichia coli maintains a cytoplasmic pH homeostasis...

show abstract

Section: Resultsmentioning

confidence: 73%

Section: Methodsmentioning

confidence: 99%

Acid Evolution of Escherichia coli K-12 Eliminates Amino Acid Decarboxylases and Reregulates Catabolism

Penix

Basting

et al. 2017

Appl Environ Microbiol

Self Cite

View full text Add to dashboard Cite

show abstract

“…An informative approach to examine the genomic basis of stress response is experimental 62 laboratory evolution (17)(18)(19)(20)(21)(22)(23). Experimental evolution of bacteria reveals changes in phenotype 63 and genotype in response to specific stressors in a controlled environment, such as carbon source 64 limitation or extreme pH.…”

Section: Importance 36mentioning

confidence: 99%

“…But 2,000 generations of E. 68 coli evolution at pH 4.8 select for loss of three acid-inducible amino-acid decarboxylase systems 69 (21). A membrane-permeant acid, benzoic acid induces glutamate decarboxylase and drug 70 resistance regulons; yet these systems are lost or downregulated during experimental evolution 71 (Moore et al 2019 (20). At high external pH, E. coli survival requires the stress 72 sigma RpoS; yet generations of growth at high pH selects against RpoS expression and activity 73 (26).…”

Section: Importance 36mentioning

confidence: 99%

“…The main chromosome and the two minichromosomes had numerous target site 132 duplications (TSDs) caused by ISH element insertions (37), as well as large deletions also 133 mediated by ISH mobility ( Table 3) (42)(43)(44)(45). For comparison, in E. coli the mutations selected 134 under stress conditions often originate via insertion elements (20). In haloarchaea, ISH elements 135 are even more active and cause numerous large-scale mutation events (46).…”

Section: Clones 126mentioning

confidence: 99%

See 1 more Smart Citation

Acid Experimental Evolution of the Extremely Halophilic Archaeon Halobacterium sp. NRC-1 Selects Mutations Affecting Arginine Transport and Catabolism

Kunka

Griffith

Holdener

et al. 2019

Preprint

Self Cite

View full text Add to dashboard Cite

16Halobacterium sp. NRC-1 (NRC-1) is an extremely halophilic archaeon that is well 17 adapted to multiple stressors such as UV, ionizing radiation, and arsenic exposure. We conducted 18 experimental evolution of NRC-1 under acid and iron stress to expand the stressors. NRC-1 was 19 serially cultured in CM+ medium modified by four stress conditions, with four evolving 20 populations per condition. At 500 generations the conditions were: optimal pH (pH 7.5), acid 21 stress (pH 6.3), iron stress (600 μM ferrous sulfate, pH 7.5), and acid plus iron stress (600 μM 22

show abstract

Salicylate, Bile Acids and Extreme Acid Cause Fitness Tradeoffs for Multidrug Pumps inEscherichia coliK-12

Lee

et al. 2020

Preprint

Self Cite

View full text Add to dashboard Cite

The aspirin derivative salicylate selects against bacterial multidrug efflux pumps of Escherichia coli K-12 such as MdtEF-TolC and EmrAB-TolC, and acid stress regulators such as GadE. Salicylate uptake is driven by the transmembrane pH gradient (ΔpH) and the proton motive force (PMF) which drives many efflux pumps. We used flow cytometry to measure the fitness tradeoffs of salicylate, bile acids, and extreme low pH for E. coli cultured with pump deletants. The AcrAB-TolC efflux pump conferred a fitness advantage in the presence of bile acids, an efflux substrate. Without bile acids, AcrA incurred a small fitness cost. The fitness advantage with bile acids was eliminated by the PMF uncoupler CCCP. The Gad acid fitness island encodes components of MdtEF-TolC (an acid-adapted efflux pump) as well as acid regulator GadE. The fitness advantage of E. coli cocultured with a Gad deletant (Δslp-gadX) was lost in the presence of salicylate. Salicylate caused an even larger fitness cost for GadE. MdtE incurred negative or neutral fitness under all media conditions, as did EmrA. But when the competition cycle included two hours at pH 2, MdtE conferred a fitness advantage. The MdtE advantage required the presence of bile acids. Thus, the MdtEF-TolC pump is useful to E. coli for transient extreme acid exposure comparable to passage through the acidic stomach. Salicylate selects against some multidrug efflux pumps, whereas bile acids selects for them; and these fitness tradeoffs are amplified by extreme acid.IMPORTANCEControl of drug resistance in gut microbial communities is a compelling problem for human health. Growth of gut bacteria is limited by host-produced acids such as bile acids, and may be modulated by plant-derived acids such as salicylic acid. Membrane-soluble organic acids can control bacterial growth by disrupting membranes, decreasing cell pH, and depleting PMF. Our flow cytometry assay measures the fitness effects of exposure to membrane-soluble organic acids, with growth cycles that may include a period of extreme acid. We find that extreme-acid exposure leads to a fitness advantage for a multidrug pump, MdtEF-TolC, which otherwise incurs a large fitness cost. Thus, organic acids and stomach acid may play important roles in controlling multidrug resistance in the gut microbiome. Therapeutic acids might be developed to limit the prevalence of multidrug resistance pumps in environmental and host-associated communities.

show abstract

Benzoate and Salicylate Tolerant Strains Lose Antibiotic Resistance during Laboratory Evolution ofEscherichia coliK-12

Abstract: 24

Cited by 5 publications

References 96 publications

Acid Evolution of Escherichia coli K-12 Eliminates Amino Acid Decarboxylases and Reregulates Catabolism

Acid Evolution of Escherichia coli K-12 Eliminates Amino Acid Decarboxylases and Reregulates Catabolism

Acid Experimental Evolution of the Extremely Halophilic Archaeon Halobacterium sp. NRC-1 Selects Mutations Affecting Arginine Transport and Catabolism

Salicylate, Bile Acids and Extreme Acid Cause Fitness Tradeoffs for Multidrug Pumps inEscherichia coliK-12

Contact Info

Product

Resources

About