Visualization of Evolutionary Stability Dynamics and Competitive Fitness of Escherichia coli Engineered with Randomized Multigene Circuits

2013 ◽  
Vol 2 (9) ◽  
pp. 519-528 ◽  
Author(s):  
Sean C. Sleight ◽  
Herbert M. Sauro
Keyword(s):  
Escherichia Coli ◽  
Evolutionary Stability ◽  
Competitive Fitness ◽  
Stability Dynamics

scholarly journals Escherichia coli Competence Gene Homologs Are Essential for Competitive Fitness and the Use of DNA as a Nutrient

2006 ◽  
Vol 188 (11) ◽  
pp. 3902-3910 ◽  
Author(s):  
Vyacheslav Palchevskiy ◽  
Steven E. Finkel
Keyword(s):  
Escherichia Coli ◽  
Sole Source ◽  
Extracellular Dna ◽  
Nutrient Source ◽  
Genetic Competence ◽  
Exogenous Dna ◽  
Competitive Fitness ◽  
E Coli ◽  
Widespread Phenomenon

ABSTRACT Natural genetic competence is the ability of cells to take up extracellular DNA and is an important mechanism for horizontal gene transfer. Another potential benefit of natural competence is that exogenous DNA can serve as a nutrient source for starving bacteria because the ability to “eat” DNA is necessary for competitive survival in environments containing limited nutrients. We show here that eight Escherichia coli genes, identified as homologs of com genes in Haemophilus influenzae and Neisseria gonorrhoeae, are necessary for the use of extracellular DNA as the sole source of carbon and energy. These genes also confer a competitive advantage to E. coli during long-term stationary-phase incubation. We also show that homologs of these genes are found throughout the proteobacteria, suggesting that the use of DNA as a nutrient may be a widespread phenomenon.

scholarly journals Fitness, Stress Resistance, and Extraintestinal Virulence in Escherichia coli

2013 ◽  
Vol 81 (8) ◽  
pp. 2733-2742 ◽  
Author(s):  
Alexandre Bleibtreu ◽  
Pierre-Alexis Gros ◽  
Cédric Laouénan ◽  
Olivier Clermont ◽  
Hervé Le Nagard ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Growth Rate ◽  
Stress Response ◽  
Mouse Model ◽  
Stress Resistance ◽  
Maximum Growth ◽  
Competitive Fitness ◽  
Content Type ◽  
General Stress Response ◽  
E Coli

ABSTRACTThe extraintestinal virulence ofEscherichia coliis dependent on numerous virulence genes. However, there is growing evidence for a role of the metabolic properties and stress responses of strains in pathogenesis. We assessed the respective roles of these factors in strain virulence by developing phenotypic assays for measuringin vitroindividual and competitive fitness and the general stress response, which we applied to 82 commensal and extraintestinal pathogenicE. colistrains previously tested in a mouse model of sepsis. Individual fitness properties, in terms of maximum growth rates in various media (Luria-Bertani broth with and without iron chelator, minimal medium supplemented with gluconate, and human urine) and competitive fitness properties, estimated as the mean relative growth rate per generation in mixed cultures with a reference fluorescentE. colistrain, were highly diverse between strains. The activity of the main general stress response regulator, RpoS, as determined by iodine staining of the colonies, H2O2resistance, andrpoSsequencing, was also highly variable. No correlation between strain fitness and stress resistance and virulence in the mouse model was found, except that the maximum growth rate in urine was higher for virulent strains. Multivariate analysis showed that the number of virulence factors was the only independent factor explaining the virulence in mice. At the species level, growth capacity and stress resistance are heterogeneous properties that do not contribute significantly to the intrinsic virulence of the strains.

scholarly journals Synthetic auxotrophy remains stable after continuous evolution and in co-culture with mammalian cells

2020 ◽  
Author(s):  
Aditya M. Kunjapur ◽  
Michael G. Napolitano ◽  
Eriona Hysolli ◽  
Karen Noguera ◽  
Evan M. Appleton ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Cell Culture ◽  
Mammalian Cell ◽  
Mammalian Cells ◽  
Mammalian Cell Culture ◽  
Normal Growth ◽  
Evolutionary Stability ◽  
Continuous Evolution ◽  
Molecule Transport ◽  
Small Molecule Transport

AbstractUnderstanding the evolutionary stability and possible context-dependence of biological containment techniques is critical as engineered microbes are increasingly under consideration for applications beyond biomanufacturing. While batch cultures of synthetic auxotrophic Escherichia coli previously exhibited undetectable escape throughout 14 days of monitoring, the long-term effectiveness of synthetic auxotrophy is unknown. Here, we report automated continuous evolution of a synthetic auxotroph using custom chemostats that supply a decreasing concentration of essential biphenylalanine (BipA). After 100 days of evolution in three separate trials, populations exhibit no observable escape and are capable of normal growth rates at 10-fold lower BipA concentration than the ancestral synthetic auxotroph. Allelic reconstruction of three proteins implicated in small molecule transport reveals their contribution to increased fitness at low BipA concentrations. Mutations do not appear in orthogonal translation machinery nor in synthetic auxotrophic markers. Based on its evolutionary stability, we introduce the progenitor synthetic auxotroph directly to mammalian cell culture. We observe containment of bacteria without detrimental effects on HEK293T cells. Overall, our findings reveal that synthetic auxotrophy is effective on timescales and in contexts that enable diverse applications.One Sentence SummaryTo ascertain whether life inevitably finds a way, we continuously evolve an Escherichia coli strain that was not able to escape from engineered biocontainment before, and we find that it does not escape even after 100 days of evolution, nor does it escape when added to mammalian cell culture.

scholarly journals Competition among Escherichia coli Strains for Space and Resources

2018 ◽  
Vol 5 (4) ◽  
pp. 93 ◽  
Author(s):  
Sarah-Jo Paquette ◽  
Rahat Zaheer ◽  
Kim Stanford ◽  
James Thomas ◽  
Tim Reuter
Keyword(s):  
Escherichia Coli ◽  
Food Industry ◽  
Mitigation Strategy ◽  
Mitigation Strategies ◽  
Natural Environments ◽  
Emerging Pathogens ◽  
Competitive Fitness ◽  
E Coli ◽  
Physical Barriers ◽  
Global Concern

Shiga toxin-producing Escherichia coli (STEC) are a subgroup of E. coli causing human diseases. Methods to control STEC in livestock and humans are limited. These and other emerging pathogens are a global concern and novel mitigation strategies are required. Habitats populated by bacteria are subjected to competition pressures due to limited space and resources but they use various strategies to compete in natural environments. Our objective was to evaluate non-pathogenic E. coli strains isolated from cattle feces for their ability to out-compete STEC. Competitive fitness of non-pathogenic E. coli against STEC were assessed in competitions using liquid, agar, and nutrient limiting assays. Winners were determined by enumeration using O-serogroup specific quantitative PCR or a semi-quantitative grading. Initial liquid competitions identified two strong non-pathogenic competitors (O103F and O26E) capable of eliminating various STEC including O157 and O111. The strain O103F was dominant across permeable physical barriers for all tested E. coli and STEC strains indicating the diffusion of antimicrobial molecules. In direct contact and even with temporal disadvantages, O103F out-competed STEC O157E. The results suggest that O103F or the diffusible molecule(s) it produces have a potential to be used as an alternative STEC mitigation strategy, either in medicine or the food industry.

scholarly journals Synthetic auxotrophy remains stable after continuous evolution and in coculture with mammalian cells

2021 ◽  
Vol 7 (27) ◽  
pp. eabf5851
Author(s):  
Aditya M. Kunjapur ◽  
Michael G. Napolitano ◽  
Eriona Hysolli ◽  
Karen Noguera ◽  
Evan M. Appleton ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Cell Culture ◽  
Growth Rates ◽  
Mammalian Cells ◽  
Mammalian Cell Culture ◽  
Normal Growth ◽  
Evolutionary Stability ◽  
Batch Cultures ◽  
Continuous Evolution

Understanding the evolutionary stability and possible context dependence of biological containment techniques is critical as engineered microbes are increasingly under consideration for applications beyond biomanufacturing. While synthetic auxotrophy previously prevented Escherichia coli from exhibiting detectable escape from batch cultures, its long-term effectiveness is unknown. Here, we report automated continuous evolution of a synthetic auxotroph while supplying a decreasing concentration of essential biphenylalanine (BipA). After 100 days of evolution, triplicate populations exhibit no observable escape and exhibit normal growth rates at 10-fold lower BipA concentration than the ancestral synthetic auxotroph. Allelic reconstruction reveals the contribution of three genes to increased fitness at low BipA concentrations. Based on its evolutionary stability, we introduce the progenitor strain directly to mammalian cell culture and observe containment of bacteria without detrimental effects on HEK293T cells. Overall, our findings reveal that synthetic auxotrophy is effective on time scales and in contexts that enable diverse applications.

scholarly journals Sxy Induces a CRP-S Regulon in Escherichia coli

2009 ◽  
Vol 191 (16) ◽  
pp. 5180-5195 ◽  
Author(s):  
Sunita Sinha ◽  
Andrew D. S. Cameron ◽  
Rosemary J. Redfield
Keyword(s):  
Escherichia Coli ◽  
Transcriptional Activation ◽  
Dna Uptake ◽  
Competitive Fitness ◽  
E Coli ◽  
Type Iv ◽  
Type Iv Pilin ◽  
Transcriptional Units ◽  
Sigma H

ABSTRACT Escherichia coli is not considered naturally competent, yet it has homologues of the genes that most competent bacteria use for DNA uptake and processing. In Haemophilus influenzae and Vibrio cholerae, these genes are regulated by the Sxy and cyclic AMP receptor (CRP) proteins. We used microarrays to find out whether similar regulation occurs in E. coli. Expression of sxy strongly induced 63 transcriptional units, 34 of which required CRP for transcriptional activation and had promoter sites resembling the Sxy- and CRP-dependent CRP-S motif previously characterized in H. influenzae. As previously reported, sxy expression also induced the sigma-H regulon. Flagellar operons were downregulated by sxy expression, although motility remained unaffected. The CRP-S regulon included all of E. coli's known competence gene homologues, so we investigated Sxy's effect on competence-associated phenotypes. A sxy knockout reduced both “natural” plasmid transformation and competitive fitness in long-term culture. In addition, expression of plasmid-borne sxy led to production of type IV pilin, the main subunit of the DNA uptake machinery of most bacteria. Although H. influenzae Sxy only weakly activated the E. coli Sxy regulon, induction was dramatically improved when it was coexpressed with its cognate CRP, suggesting that intimate interactions between Sxy and CRP are required for transcriptional activation at CRP-S sites.

scholarly journals The Effects of Colicin Production Rates on Allelopathic Interactions in Escherichia coli Populations

2019 ◽  
Vol 7 (11) ◽  
pp. 564 ◽  
Author(s):  
Ghazaryan ◽  
Giladi ◽  
Gillor
Keyword(s):  
Escherichia Coli ◽  
Production Rates ◽  
Competitive Fitness ◽  
Living Space ◽  
Bacteriocin Producer ◽  
Unstructured Environment ◽  
Beneficial Traits ◽  
Allelopathic Interactions ◽  
Sensitive Population ◽  
Space Competition

Allelopathic interactions mediated by bacteriocins production serve microorganisms in the never-ending battle for resources and living space. Competition between the bacteriocin producer and sensitive populations results in the exclusion of one or the other depending on their initial frequencies, the structure of their habitat, their community density and their nutrient availability. These interactions were extensively studied in bacteriocins produced by Escherichia coli, the colicins. In spatially structured environments where interactions are local, colicin production has been shown to be advantageous to the producer population, allowing them to compete even when initially rare. Yet, in a well-mixed, unstructured environment where interactions are global, rare producer populations cannot invade a common sensitive population. Here we are showing, through an experimental model, that colicin-producers can outcompete sensitive and producer populations when the colicin production rates are enhanced. In fact, colicin production rates were proportional to the producer competitive fitness and their overall success in out-competing opponents when invading at very low initial frequencies. This ability of rare populations to invade established communities maintains diversity and allows the dispersal of beneficial traits.

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