Experimental evolution of gallium resistance in Escherichia coli

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

doi:10.1093/emph/eoz025

Cited by 22 publications

(29 citation statements)

References 47 publications

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“…However, in prior studies we have deployed more direct methods to test whether the genomic variants we discovered should and actually do confer resistance. For example, we have utilized computational modeling of 3-dimensional structures of altered proteins to test their affinity for ionic metals [ 12 , 15 , 42 ]. These studies showed the alteration in the protein caused by the variant resulting from the selective sweep did reduce or increase the affinity to the target metal compared to the controls/ancestor.…”

Section: Discussionmentioning

confidence: 99%

“…E. coli MG1655 (ATCC #47076) was used in this study because it does not have plasmids and its circular chromosome is composed of 4,641,652 nucleotides (GenBank: GenBank: 117 NC_000913.3; Riley et al 2006). All of our previous studies of ionic and nanoparticle resistance have used this strain [ 13 , 14 , 15 ]. This strain is the ancestor of all the selection treatments (FeNP and Controls) evaluated in this study.…”

Section: Methodsmentioning

confidence: 99%

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Experimental Evolution of Magnetite Nanoparticle Resistance in Escherichia coli

et al. 2021

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Both ionic and nanoparticle iron have been proposed as materials to control multidrug-resistant (MDR) bacteria. However, the potential bacteria to evolve resistance to nanoparticle bacteria remains unexplored. To this end, experimental evolution was utilized to produce five magnetite nanoparticle-resistant (FeNP1–5) populations of Escherichia coli. The control populations were not exposed to magnetite nanoparticles. The 24-h growth of these replicates was evaluated in the presence of increasing concentrations magnetite NPs as well as other ionic metals (gallium III, iron II, iron III, and silver I) and antibiotics (ampicillin, chloramphenicol, rifampicin, sulfanilamide, and tetracycline). Scanning electron microscopy was utilized to determine cell size and shape in response to magnetite nanoparticle selection. Whole genome sequencing was carried out to determine if any genomic changes resulted from magnetite nanoparticle resistance. After 25 days of selection, magnetite resistance was evident in the FeNP treatment. The FeNP populations also showed a highly significantly (p < 0.0001) greater 24-h growth as measured by optical density in metals (Fe (II), Fe (III), Ga (III), Ag, and Cu II) as well as antibiotics (ampicillin, chloramphenicol, rifampicin, sulfanilamide, and tetracycline). The FeNP-resistant populations also showed a significantly greater cell length compared to controls (p < 0.001). Genomic analysis of FeNP identified both polymorphisms and hard selective sweeps in the RNA polymerase genes rpoA, rpoB, and rpoC. Collectively, our results show that E. coli can rapidly evolve resistance to magnetite nanoparticles and that this result is correlated resistances to other metals and antibiotics. There were also changes in cell morphology resulting from adaptation to magnetite NPs. Thus, the various applications of magnetite nanoparticles could result in unanticipated changes in resistance to both metal and antibiotics.

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Section: Discussionmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Experimental Evolution of Magnetite Nanoparticle Resistance in Escherichia coli

et al. 2021

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“…Both G210C and A526T were also detected in our 45-day iron (II) adapted populations [ 27 ]. In red are two mutations (N169K and G400S) which were detected in gallium (iron analog) resistant strains [ 38 ] and as shown, map to similar regions as the iron resistant mutations. ( B ) The iron-citrate complexed structure (PDB1PO3) was also used to map two of the three iron resistant residues (D87Y lies in an unstructured region and therefore could not be mapped) and the gallium mutations.…”

Section: Discussionmentioning

confidence: 99%

“…Second, gallium is an iron analog. In our previous work, this strain of E. coli also acquires mutations in fecA as a result of gallium resistance which could account for the increased optical densities in the adapted strain in the metal [ 38 ]. What is most concerning is the multi-drug resistance acquired in this strain, which indicates that these strains have the potential to be even more harmful than originally anticipated.…”

Section: Discussionmentioning

confidence: 99%

Too much of a good thing

Thomas

Ewunkem

Boyd

et al. 2021

Evolution, Medicine, and Public Health

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Background There has been an increased usage of metallic antimicrobial materials to control pathogenic and multidrug resistant bacteria. Yet, there is a corresponding need to know if this usage leads to genetic adaptations that could produce more harmful strains. Methodology Experimental evolution was used to adapt Escherichia coli K-12 MG1655 to excess iron (II) with subsequent genomic analysis. Phenotypic assays and gene expression studies were conducted to demonstrate pleiotropic effects associated with this adaptation and to elucidate potential cellular responses. Results After 200 days of adaptation, populations cultured in excess iron (II), showed a significant increase in 24-hour optical densities compared to controls. Furthermore, these populations showed increased resistance towards other metals (iron (III) and gallium (III)) and to traditional antibiotics (bacitracin, rifampin, chloramphenicol and sulfanilamide). Genomic analysis identified selective sweeps in three genes; fecA, ptsP and ilvG unique to the iron (II) resistant populations, and gene expression studies demonstrated that their cellular response may be to downregulate genes involved in iron transport (cirA and fecA) while increasing the oxidative stress response (oxyR, soxS and soxR) prior to FeSO4 exposure. Conclusions and Implications Together, this indicates that the selected populations can quickly adapt to stressful levels of iron (II). This study is unique in that it demonstrates that E. coli can adapt to environments that contain excess levels of an essential micronutrient while also demonstrating the genomic foundations of the response and the pleiotropic consequences. The fact that adaptation to excess iron also causes increases in general antibiotic resistance is a serious concern.

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“…Adaptive evolution strategy can be used to obtain strains with an evident product tolerance, [ 81 ] substrate utilization, and cell survival phenotype after evolution. [ 40,82 ] The goal of adaptive evolution is to obtain transporter mutants with higher transport efficiency, substrate specificity, or conversely, mutants with better substrate compatibility. For instance, an adaptive evolution was conducted using the hexose transporter CiGXS1 FIM in yeasts, and glucose–xylose cotransport mutants were selected based on their survival on xylose and glucose plates.…”

Section: Transporter Engineering In Microbial Cellsmentioning

confidence: 99%

Transporter Engineering for Microbial Manufacturing

Zhu

Zhou

Wang

et al. 2020

Biotechnology Journal

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Microbes play an important role in biotransformation and biosynthesis of biofuels, natural products, and polymers. Therefore, microbial manufacturing has been widely used in medicine, industry, and agriculture. However, common strategies including enzyme engineering, pathway optimization, and host engineering are generally inadequate to obtain an efficient microbial production system. Transporter engineering provides an alternative strategy to promote the transmembrane transfer of substrates, intermediates, and final products in microbial cells and thus enhances production by alleviating feedback inhibition and cytotoxicity caused by final products. According to the current studies in transport engineering, native transporters usually have low expression and poor transportation ability, resulting in inefficient transport processes and microbial production. In this review, current approaches for transporter mining, characterization, and verification are comprehensively summarized. Practical approaches to enhance the transport system in engineered cells, such as balancing transporter overexpression and cell growth, and evolution of native transporters are discussed. Furthermore, the applications of transporter engineering in microbial manufacturing, including enhancement of substrate utilization, concentration of metabolic flux to the target pathway, and acceleration of efflux and recovery of products, demonstrate its outstanding advantages and promising prospects.

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Experimental evolution of gallium resistance in Escherichia coli

Cited by 22 publications

References 47 publications

Experimental Evolution of Magnetite Nanoparticle Resistance in Escherichia coli

Experimental Evolution of Magnetite Nanoparticle Resistance in Escherichia coli

Too much of a good thing

Transporter Engineering for Microbial Manufacturing

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