Bacterial Response to Copper in the Environment: Copper Resistance in Escherichia coli as a Model System

1990 ◽  
pp. 625-632 ◽  
Author(s):  
B. T. O. Lee ◽  
N. L. Brown ◽  
S. Rogers ◽  
A. Bergemann ◽  
J. Camakaris ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Model System ◽  
Copper Resistance ◽  
Bacterial Response

scholarly journals Pathovar Transcriptomes

mSystems ◽  
2017 ◽  
Vol 2 (4) ◽  
Author(s):  
Amy Platenkamp ◽  
Jay L. Mellies
Keyword(s):  
Gene Expression ◽  
Escherichia Coli ◽  
Regulatory Networks ◽  
Virulence Gene ◽  
Model System ◽  
Genomic Sequences ◽  
Bacterial Strains ◽  
Content Type ◽  
Virulence Gene Expression ◽  
Link Type

ABSTRACT Archetypal pathogenic bacterial strains are often used to elucidate regulatory networks of an entire pathovar, which encompasses multiple lineages and phylogroups. With enteropathogenic Escherichia coli (EPEC) as a model system, Hazen and colleagues (mSystems 6:e00024-17, 2017, https://doi.org/10.1128/mSystems.00024-17 ) used 9 isolates representing 8 lineages and 3 phylogroups to find that isolates with similar genomic sequences exhibit similarities in global transcriptomes under conditions of growth in medium that induces virulence gene expression, and they found variation among individual isolates. Archetypal pathogenic bacterial strains are often used to elucidate regulatory networks of an entire pathovar, which encompasses multiple lineages and phylogroups. With enteropathogenic Escherichia coli (EPEC) as a model system, Hazen and colleagues (mSystems 6:e00024-17, 2017, https://doi.org/10.1128/mSystems.00024-17 ) used 9 isolates representing 8 lineages and 3 phylogroups to find that isolates with similar genomic sequences exhibit similarities in global transcriptomes under conditions of growth in medium that induces virulence gene expression. They also found variation among individual isolates. Their work illustrates the importance of moving beyond observing regulatory phenomena of a limited number of regulons in a few archetypal strains, with the possibility of correlating clinical symptoms to key transcriptional pathways across lineages and phylogroups.

Escherichia coli CopA N-Terminal Cys(X)2Cys Motifs Are Not Required for Copper Resistance or Transport

2001 ◽  
Vol 286 (2) ◽  
pp. 414-418 ◽  
Author(s):  
Bin Fan ◽  
Gregor Grass ◽  
Christopher Rensing ◽  
Barry P. Rosen
Keyword(s):  
Escherichia Coli ◽  
Copper Resistance

scholarly journals Breaking through evolutionary constraint by environmental fluctuations

2015 ◽  
Author(s):  
Marjon GJ de Vos ◽  
Alexandre Dawid ◽  
Vanda Sunderlikova ◽  
Sander J Tans
Keyword(s):  
Escherichia Coli ◽  
Environmental Variability ◽  
Model System ◽  
Evolutionary Constraint ◽  
Apparent Paradox ◽  
Epistatic Interactions ◽  
Genetic Constraints ◽  
Trade Offs ◽  
Fluctuating Environments ◽  
Genetic Constraint

Epistatic interactions can frustrate and shape evolutionary change. Indeed, phenotypes may fail to evolve because essential mutations can only be selected positively if fixed simultaneously. How environmental variability affects such constraints is poorly understood. Here we studied genetic constraints in fixed and fluctuating environments, using theEscherichia coli lacoperon as a model system for genotype-environment interactions. The data indicated an apparent paradox: in different fixed environments, mutational trajectories became trapped at sub-optima where no further improvements were possible, while repeated switching between these same environments allowed unconstrained adaptation by continuous improvements. Pervasive cross-environmental trade-offs transformed peaks into valleys upon environmental change, thus enabling escape from entrapment. This study shows that environmental variability can lift genetic constraint, and that trade-offs not only impede but can also facilitate adaptive evolution.

scholarly journals High-resolution crystal structures of Escherichia coli FtsZ bound to GDP and GTP

2020 ◽  
Vol 76 (2) ◽  
pp. 94-102 ◽  
Author(s):  
Maria A. Schumacher ◽  
Tomoo Ohashi ◽  
Lauren Corbin ◽  
Harold P. Erickson
Keyword(s):  
Escherichia Coli ◽  
Staphylococcus Aureus ◽  
Cell Division ◽  
High Resolution ◽  
Crystal Structures ◽  
Bacterial Cell ◽  
Model System ◽  
E Coli ◽  
Z Ring ◽  
Main Model

Bacterial cytokinesis is mediated by the Z-ring, which is formed by the prokaryotic tubulin homolog FtsZ. Recent data indicate that the Z-ring is composed of small patches of FtsZ protofilaments that travel around the bacterial cell by treadmilling. Treadmilling involves a switch from a relaxed (R) state, favored for monomers, to a tense (T) conformation, which is favored upon association into filaments. The R conformation has been observed in numerous monomeric FtsZ crystal structures and the T conformation in Staphylococcus aureus FtsZ crystallized as assembled filaments. However, while Escherichia coli has served as a main model system for the study of the Z-ring and the associated divisome, a structure has not yet been reported for E. coli FtsZ. To address this gap, structures were determined of the E. coli FtsZ mutant FtsZ(L178E) with GDP and GTP bound to 1.35 and 1.40 Å resolution, respectively. The E. coli FtsZ(L178E) structures both crystallized as straight filaments with subunits in the R conformation. These high-resolution structures can be employed to facilitate experimental cell-division studies and their interpretation in E. coli.

scholarly journals Genomewide Mutational Diversity in Escherichia coli Population Evolving in Prolonged Stationary Phase

mSphere ◽  
2017 ◽  
Vol 2 (3) ◽  
Author(s):  
Savita Chib ◽  
Farhan Ali ◽  
Aswin Sai Narain Seshasayee
Keyword(s):  
Escherichia Coli ◽  
Genetic Diversity ◽  
Stationary Phase ◽  
Phenotypic Diversity ◽  
Model System ◽  
Content Type ◽  
Neutral Drift ◽  
E Coli ◽  
Evolution By Natural Selection ◽  
Over Time

ABSTRACT Prolonged stationary phase in bacteria, contrary to its name, is highly dynamic, with extreme nutrient limitation as a predominant stress. Stationary-phase cultures adapt by rapidly selecting a mutation(s) that confers a growth advantage in stationary phase (GASP). The phenotypic diversity of starving E. coli populations has been studied in detail; however, only a few mutations that accumulate in prolonged stationary phase have been described. This study documented the spectrum of mutations appearing in Escherichia coli during 28 days of prolonged starvation. The genetic diversity of the population increases over time in stationary phase to an extent that cannot be explained by random, neutral drift. This suggests that prolonged stationary phase offers a great model system to study adaptive evolution by natural selection. Prolonged stationary phase is an approximation of natural environments presenting a range of stresses. Survival in prolonged stationary phase requires alternative metabolic pathways for survival. This study describes the repertoire of mutations accumulating in starving Escherichia coli populations in lysogeny broth. A wide range of mutations accumulates over the course of 1 month in stationary phase. Single nucleotide polymorphisms (SNPs) constitute 64% of all mutations. A majority of these mutations are nonsynonymous and are located at conserved loci. There is an increase in genetic diversity in the evolving populations over time. Computer simulations of evolution in stationary phase suggest that the maximum frequency of mutations observed in our experimental populations cannot be explained by neutral drift. Moreover, there is frequent genetic parallelism across populations, suggesting that these mutations are under positive selection. Finally, functional analysis of mutations suggests that regulatory mutations are frequent targets of selection. IMPORTANCE Prolonged stationary phase in bacteria, contrary to its name, is highly dynamic, with extreme nutrient limitation as a predominant stress. Stationary-phase cultures adapt by rapidly selecting a mutation(s) that confers a growth advantage in stationary phase (GASP). The phenotypic diversity of starving E. coli populations has been studied in detail; however, only a few mutations that accumulate in prolonged stationary phase have been described. This study documented the spectrum of mutations appearing in Escherichia coli during 28 days of prolonged starvation. The genetic diversity of the population increases over time in stationary phase to an extent that cannot be explained by random, neutral drift. This suggests that prolonged stationary phase offers a great model system to study adaptive evolution by natural selection.

scholarly journals Sandwich Hybridization Assay for Sensitive Detection of Dynamic Changes in mRNA Transcript Levels in Crude Escherichia coli Cell Extracts in Response to Copper Ions

2008 ◽  
Vol 74 (24) ◽  
pp. 7463-7470 ◽  
Author(s):  
Daniel Thieme ◽  
Peter Neubauer ◽  
Dietrich H. Nies ◽  
Gregor Grass
Keyword(s):  
Escherichia Coli ◽  
Alkaline Phosphatase ◽  
Time Course ◽  
Copper Ions ◽  
Copper Resistance ◽  
Hybridization Assay ◽  
Target Mrna ◽  
Cell Extracts ◽  
Sandwich Hybridization ◽  
Sandwich Hybridization Assay

ABSTRACT Transcript quantification techniques usually rely on purified mRNAs. We report here a solution-based sandwich hybridization assay for the quantification of mRNAs from Escherichia coli without the need of prior RNA isolation. This assay makes use of four DNA oligonucleotide probes adjacently hybridizing to target RNA in clarified cell extracts. Two helper probes facilitate the hybridization of a detection and a capture probe. The latter is biotin labeled, allowing binding to streptavidin-coated paramagnetic beads and the separation of the RNA-DNA hybrid from cellular constituents. Added antidigoxigenin Fab fragments conjugated to alkaline phosphatase bind to the digoxigenin-labeled detection probe, completing the sandwich of the paramagnetic bead, mRNA, probes, and alkaline phosphatase. The target transcript can be quantified by assessing phosphatase activity on a substrate that is converted into a fluorescent product. The amount of target mRNA is calculated from the fluorescence output and from a calibration curve for a known concentration of in vitro-synthesized target mRNA. This technique was used in time course experiments to investigate the expression of three genes responsible for the copper resistance of E. coli. The induction of gene expression by copper cations was rapid, but under aerobic conditions, the levels of expression returned to low, prestress levels within minutes. In anaerobiosis, high-level expression continued for at least 1 h. When cultures were shifted from anaerobiosis to aerobiosis, expression levels were diminished within minutes to prestress levels. The improved technique presented here is relatively simple, has very high degrees of sensitivity and robustness, is less laborious than other RNA quantification methods, and is not negatively affected by genomic DNA. These characteristics make it a powerful complementary application to genetic reporter fusions and to reverse transcription-PCR.

Effects of Plant-Derived Extracts, Other Antimicrobials, and Their Combinations against Escherichia coli O157:H7 in Beef Systems

2015 ◽  
Vol 78 (6) ◽  
pp. 1090-1097 ◽  
Author(s):  
KYUNG YUK KO ◽  
IFIGENIA GEORNARAS ◽  
HYUN-DONG PAIK ◽  
KEE-TAE KIM ◽  
JOHN N. SOFOS
Keyword(s):  
Escherichia Coli ◽  
Lactic Acid ◽  
Untreated Control ◽  
Sodium Tripolyphosphate ◽  
Model System ◽  
Surface Contamination ◽  
Escherichia Coli O157 ◽  
E Coli ◽  
Blade Tenderization ◽  
Sodium Diacetate

The antimicrobial effects of thyme oil (TO), grapefruit seed extract (GSE), and basil essential oil, alone or in combination with cetylpyridinium chloride (CPC), sodium diacetate, or lactic acid, were evaluated against Escherichia coli O157:H7 in a moisture-enhanced beef model system. The model system was composed of a nonsterile beef homogenate to which NaCl (0.5%) and sodium tripolyphosphate (0.25%) were added, together with the tested antimicrobial ingredients. Beef homogenate treatments were inoculated (ca. 3 log CFU/ml) with rifampin-resistant E. coli O157:H7 (eight-strain mixture) and incubated at 15°C (48 h). The most effective individual treatments were TO (0.25 or 0.5%) and GSE (0.5 or 1.0%), which immediately reduced (P < 0.05) pathogen levels by ≥3.4 log CFU/ml. Additionally, CPC (0.04%) reduced initial E. coli O157:H7 counts by 2.7 log CFU/ml. Most combinations of the tested plant-derived extracts with CPC (0.02 or 0.04%) and sodium diacetate (0.25%) had an additive effect with respect to antibacterial activity. In a second study, antimicrobial interventions were evaluated for their efficacy in reducing surface contamination of E. coli O157:H7 on beef cuts and to determine the effect of these surface treatments on subsequent internalization of the pathogen during blade tenderization. Beef cuts (10 by 8 by 3.5 cm) were inoculated (ca. 4 log CFU/g) on one side with the rifampin-resistant E. coli O157:H7 strain mixture and were then spray treated (20 lb/in2, 10 s) with water, GSE (5 and 10%), lactic acid (5%), or CPC (5%). Untreated (control) and spray-treated surfaces were then subjected to double-pass blade tenderization. Surface contamination (4.4 log CFU/g) of E. coli O157:H7 was reduced (P < 0.05) to 3.4 (5% CPC) to 4.1 (water or 5% GSE) log CFU/g following spray treatment. The highest and lowest transfer rates of pathogen cells from the surface to deeper tissues of blade-tenderized sections were obtained in the untreated control and CPC-treated samples, respectively.

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