Experimental evolution of gallium resistance in Escherichia coli

Joseph L Graves Jr; Akamu J Ewunkem; Jason Ward; Constance Staley; Misty D Thomas; Kristen L Rhinehardt; Jian Han; Scott H Harrison

doi:10.1093/emph/eoz025

Experimental evolution of gallium resistance in Escherichia coli

Evol Med Public Health. 2019 Sep 6;2019(1):169-180. doi: 10.1093/emph/eoz025. eCollection 2019.

Authors

Joseph L Graves Jr^{1

2}, Akamu J Ewunkem^{1

2}, Jason Ward³, Constance Staley⁴, Misty D Thomas^{2

5}, Kristen L Rhinehardt^{1

2}, Jian Han^{2

5}, Scott H Harrison^{2

5}

Affiliations

¹ Department of Nanoengineering, Joint School of Nanoscience & Nanoengineering, North Carolina A&T State University & UNC Greensboro, Greensboro, NC, USA.
² BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, MI, USA.
³ High School Science Teacher, Davie Public High School, Davie, NC, USA.
⁴ Department of Biology, Bennett College, Greensboro, NC, USA.
⁵ Department of Biology, North Carolina A&T State University, Greensboro, NC, USA.

Abstract

Background and objectives: Metallic antimicrobial materials are of growing interest due to their potential to control pathogenic and multidrug-resistant bacteria. Yet we do not know if utilizing these materials can lead to genetic adaptations that produce even more dangerous bacterial varieties.

Methodology: Here we utilize experimental evolution to produce strains of Escherichia coli K-12 MG1655 resistant to, the iron analog, gallium nitrate (Ga(NO₃)₃). Whole genome sequencing was utilized to determine genomic changes associated with gallium resistance. Computational modeling was utilized to propose potential molecular mechanisms of resistance.

Results: By day 10 of evolution, increased gallium resistance was evident in populations cultured in medium containing a sublethal concentration of gallium. Furthermore, these populations showed increased resistance to ionic silver and iron (III), but not iron (II) and no increase in traditional antibiotic resistance compared with controls and the ancestral strain. In contrast, the control populations showed increased resistance to rifampicin relative to the gallium-resistant and ancestral population. Genomic analysis identified hard selective sweeps of mutations in several genes in the gallium (III)-resistant lines including: fecA (iron citrate outer membrane transporter), insl1 (IS30 tranposase) one intergenic mutations arsC →/→ yhiS; (arsenate reductase/pseudogene) and in one pseudogene yedN ←; (iapH/yopM family). Two additional significant intergenic polymorphisms were found at frequencies > 0.500 in fepD ←/→ entS (iron-enterobactin transporter subunit/enterobactin exporter, iron-regulated) and yfgF ←/→ yfgG (cyclic-di-GMP phosphodiesterase, anaerobic/uncharacterized protein). The control populations displayed mutations in the rpoB gene, a gene associated with rifampicin resistance.

Conclusions: This study corroborates recent results observed in experiments utilizing pathogenic Pseudomonas strains that also showed that Gram-negative bacteria can rapidly evolve resistance to an atom that mimics an essential micronutrient and shows the pleiotropic consequences associated with this adaptation.

Lay summary: We utilize experimental evolution to produce strains of Escherichia coli K-12 MG1655 resistant to, the iron analog, gallium nitrate (Ga(NO₃)₃). Whole genome sequencing was utilized to determine genomic changes associated with gallium resistance. Computational modeling was utilized to propose potential molecular mechanisms of resistance.

Keywords: Escherichia coli; experimental evolution; gallium; genomics.