scholarly journals Emerging Adaptive Strategies Under Temperature Fluctuations in a Laboratory Evolution Experiment of Escherichia Coli

2021 ◽  
Vol 12 ◽  
Author(s):  
Maryl Lambros ◽  
Ximo Pechuan-Jorge ◽  
Daniel Biro ◽  
Kenny Ye ◽  
Aviv Bergman
Keyword(s):  
Escherichia Coli ◽  
Genetic Background ◽  
Gene Mutations ◽  
Periodic Regime ◽  
Environmental Fluctuation ◽  
Laboratory Evolution ◽  
Array Measurements ◽  
Evolution Experiment ◽  
Two Temperatures ◽  
Different Strains

Generalists and specialists are types of strategies individuals can employ that can evolve in fluctuating environments depending on the extremity and periodicity of the fluctuation. To evaluate whether the evolution of specialists or generalists occurs under environmental fluctuation regimes with different levels of periodicity, 24 populations of Escherichia coli underwent laboratory evolution with temperatures alternating between 15 and 43°C in three fluctuation regimes: two periodic regimes dependent on culture's cell density and one random (non-periodic) regime with no such dependency, serving as a control. To investigate contingencies on the genetic background, we seeded our experiment with two different strains. After the experiment, growth rate measurements at the two temperatures showed that the evolution of specialists was favored in the random regime, while generalists were favored in the periodic regimes. Whole genome sequencing demonstrated that several gene mutations were selected in parallel in the evolving populations with some dependency on the starting genetic background. Given the genes mutated, we hypothesized that the driving force behind the observed adaptations is the restoration of the internal physiology of the starting strains' unstressed states at 37°C, which may be a means of improving fitness in the new environments. Phenotypic array measurements supported our hypothesis by demonstrating a tendency of the phenotypic response of the evolved strains to move closer to the starting strains' response at the optimum of 37°C, especially for strains classified as generalists.

scholarly journals Evolutionary contingency’s impact on laboratory evolution ofEscherichia coliunder fluctuating environments

2019 ◽  
Author(s):  
Ximo Pechuan ◽  
Daniel Biro ◽  
Maryl Lambros ◽  
Aviv Bergman
Keyword(s):  
Escherichia Coli ◽  
Environmental Conditions ◽  
Phenotypic Characterization ◽  
General Tendency ◽  
Environmental Fluctuation ◽  
Laboratory Evolution ◽  
Phenotypic Response ◽  
Final Population ◽  
Fluctuating Environments ◽  
Environmental Fluctuations

1AbstractThe adaptation of biological organisms to fluctuating environments is one major determinant of their structural and dynamical complexity. Organisms have evolved devoted adaptations to ensure the robust performance of physiological functions under environmental fluctuations. To further our understanding of particular adaptation strategies to different environmental fluctuations, we perform laboratory evolution experiments ofEscherichia coliunder three temperature fluctuation regimes alternating between 15°C and 43°C. Two of these regimes are determined by the population’s growth, while the third regime switches stochastically. To address evolutionary contingencies, the experiments are performed on two lineages departing from different genetic backgrounds. The two lineages display distinct evolutionary trajectories, demonstrating dependency on the starting strain’s genetic background. Several genes exhibit a high degree of parallelism, suggesting their potential adaptive nature. The growth increase of the representative clones from each final population relative to their ancestor at 15°C and 43°C demonstrated no correlation between both temperatures, insinuating an absence of a strong trade-off between these two temperatures. Some had a growth rate decrease at 15°C unless exposed to a 43°C epoch, indicating some degree of internalization of the structure of the environment fluctuations. The phenotypic response of the evolved clones at 15°C and 43°C was assessed by a phenotype array method. The resulting responses reveal a general tendency to move closer to the phenotypic response of our starting strains at the optimum of 37°C. This observation expands the documented restorative responses, even when facing complex environmental conditions.2Author SummaryLaboratory evolution experiments have been widely employed to test hypotheses from evolutionary theory. To assess the dynamics of adaptation under environmental fluctuations, we evolved 24Escherichia colipopulations under different regimes of temperature switching between 15°C and 43°C for about 600 generations. At the final point of the evolution experiment, the evolved populations were genome sequenced and clones were isolated and sequenced for phenotypic characterization. Fitness measurements revealed adaptation to both environmental conditions and some strains internalized the environmental fluctuation. Array phenotypic measurements showed that the majority of evolved strains tended to restore the phenotypic signature of the perturbed environments to that of the optimal temperature condition. This observation expands the documented restorative responses, even when facing complex environmental conditions.

Analysis of differentially upregulated proteins in ptsHIcrr− and rppH− mutants in Escherichia coli during an adaptive laboratory evolution experiment

2018 ◽  
Vol 102 (23) ◽  
pp. 10193-10208 ◽  
Author(s):  
César Aguilar ◽  
Gabriel Martínez-Batallar ◽  
Noemí Flores ◽  
Fabián Moreno-Avitia ◽  
Sergio Encarnación ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Adaptive Laboratory Evolution ◽  
Laboratory Evolution ◽  
Evolution Experiment

Polyester Cloth–Based Hybridization Array System for Identification of Enterohemorrhagic Escherichia coli Serogroups O26, O45, O103, O111, O121, O145, and O157

2012 ◽  
Vol 75 (9) ◽  
pp. 1691-1697 ◽  
Author(s):  
BURTON W. BLAIS ◽  
MARTINE GAUTHIER ◽  
MYLÈNE DESCHÊNES ◽  
GEORGE HUSZCZYNSKI
Keyword(s):  
Escherichia Coli ◽  
Marker Gene ◽  
Enterohemorrhagic Escherichia Coli ◽  
Oligonucleotide Probes ◽  
E Coli ◽  
Polyester Cloth ◽  
Gene Profiles ◽  
Pcr Products ◽  
Different Strains ◽  
Immunoenzymatic Assay

A cloth-based hybridization array system (CHAS) was developed for the identification of foodborne colony isolates of seven priority enterohemorrhagic Escherichia coli (EHEC-7) serogroups targeted by U.S. food inspection programs. Gene sequences associated with intimin; Shiga-like toxins 1 and 2; and the antigenic markers O26, O45, O103, O111, O121, O145, and O157 were amplified in a multiplex PCR incorporating a digoxigenin label, and detected by hybridization of the PCR products with an array of specific oligonucleotide probes immobilized on a polyester cloth support, with subsequent immunoenzymatic assay of the captured amplicons. The EHEC-7 CHAS exhibited 100% inclusivity and 100% exclusivity characteristics with respect to detection of the various markers among 89 different E. coli strains, with various marker gene profiles and 15 different strains of non–E. coli bacteria.

scholarly journals Application of Bacteriophages on Shiga Toxin-Producing Escherichia coli (STEC) Biofilm

Antibiotics ◽  
2021 ◽  
Vol 10 (11) ◽  
pp. 1423
Author(s):  
Nicola Mangieri ◽  
Roberto Foschino ◽  
Claudia Picozzi
Keyword(s):  
Escherichia Coli ◽  
Shiga Toxin ◽  
Biofilm Formation ◽  
Pathogenic Bacteria ◽  
Antimicrobial Agents ◽  
Bacterial Cells ◽  
Abiotic Surfaces ◽  
Continuous Presence ◽  
Different Strains ◽  
Better Than

Shiga toxin-producing Escherichia coli are pathogenic bacteria able to form biofilms both on abiotic surfaces and on food, thus increasing risks for food consumers. Moreover, biofilms are difficult to remove and more resistant to antimicrobial agents compared to planktonic cells. Bacteriophages, natural predators of bacteria, can be used as an alternative to prevent biofilm formation or to remove pre-formed biofilm. In this work, four STEC able to produce biofilm were selected among 31 different strains and tested against single bacteriophages and two-phage cocktails. Results showed that our phages were able to reduce biofilm formation by 43.46% both when used as single phage preparation and as a cocktail formulation. Since one of the two cocktails had a slightly better performance, it was used to remove pre-existing biofilms. In this case, the phages were unable to destroy the biofilms and reduce the number of bacterial cells. Our data confirm that preventing biofilm formation in a food plant is better than trying to remove a preformed biofilm and the continuous presence of bacteriophages in the process environment could reduce the number of bacteria able to form biofilms and therefore improve the food safety.

scholarly journals Efficient production of (S)-1-phenyl-1, 2-ethanediol using xylan as co-substrate by a coupled multi-enzyme Escherichia coli system

2020 ◽  
Author(s):  
Junchao Rao ◽  
Rongzhen Zhang ◽  
Guanyu Xu ◽  
Lihong Li ◽  
Yan Xu
Keyword(s):  
Escherichia Coli ◽  
Glucose Dehydrogenase ◽  
Optical Purity ◽  
Carbonyl Reductase ◽  
Cofactor Regeneration ◽  
Efficient Production ◽  
Chiral Synthesis ◽  
E Coli ◽  
Concomitant Reduction ◽  
Different Strains

Abstract Background: ( S )-1-phenyl-1,2-ethanediol is an important chiral intermediate in the synthesis of liquid crystals and chiral biphosphines.(S)-carbonyl reductase II from Candida parapsilosis catalyzes the conversion of 2-hydroxyacetophenone to ( S )-1-phenyl-1,2-ethanediol with NADPH as a cofactor. Glucose dehydrogenase with a Ala258Phe mutation is able to catalyze the oxidation of xylose with concomitant reduction of NADP + to NADPH, while endo-β-1,4-xylanase 2 catalyzes the conversion of xylan to xylose. In the present work, the Ala258Phe glucose dehydrogenase mutant and endo-β-1,4-xylanase 2 were introduced into the ( S )-carbonyl reductase II-mediated chiral pathway to strengthen cofactor regeneration by using xylan as a naturally abundant co-substrate. Results: We constructed several coupled multi-enzyme systems by introducing ( S )-carbonyl reductase II, the A258F glucose dehydrogenase mutant and endo-β-1,4-xylanase 2 into Escherichia coli . Different strains were produced by altering the location of the encoding genes on the plasmid. Only recombinant E. coli /pET-G-S-2 expressed all three enzymes, and this strain produced ( S )-1-phenyl-1,2-ethanediol from 2-hydroxyacetophenone as a substrate and xylan as a co-substrate. The optical purity was 100% and the yield was 98.3% (6 g/L 2-HAP) under optimal conditions of 35°C, pH 6.5 and a 2:1 substrate-co-substrate ratio. The introduction of A258F glucose dehydrogenase and endo-β-1,4-xylanase 2 into the ( S )-carbonyl reductase II-mediated chiral pathway caused a 54.6% increase in yield, and simultaneously reduced the reaction time from 48 h to 28 h. Conclusions: This study demonstrates efficient chiral synthesis using a pentose as a co-substrate to enhance cofactor regeneration. This provides a new approach for enantiomeric catalysis through the inclusion of naturally abundant materials.

scholarly journals Molecular Characterization of Commensal Escherichia coli Adapted to Different Compartments of the Porcine Gastrointestinal Tract

2012 ◽  
Vol 78 (19) ◽  
pp. 6799-6803 ◽  
Author(s):  
Sam Abraham ◽  
David M. Gordon ◽  
James Chin ◽  
Huub J. M. Brouwers ◽  
Peter Njuguna ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Gastrointestinal Tract ◽  
Random Amplified Polymorphic Dna ◽  
Content Type ◽  
E Coli ◽  
Plasmid Replicon ◽  
Different Strains ◽  
Different Characteristics

ABSTRACTThe role ofEscherichia colias a pathogen has been the focus of considerable study, while much less is known about it as a commensal and how it adapts to and colonizes different environmental niches within the mammalian gut. In this study, we characterizeEscherichia coliorganisms (n= 146) isolated from different regions of the intestinal tracts of eight pigs (dueodenum, ileum, colon, and feces). The isolates were typed using the method of random amplified polymorphic DNA (RAPD) and screened for the presence of bacteriocin genes and plasmid replicon types. Molecular analysis of variance using the RAPD data showed thatE. coliisolates are nonrandomly distributed among different gut regions, and that gut region accounted for 25% (P< 0.001) of the observed variation among strains. Bacteriocin screening revealed that a bacteriocin gene was detected in 45% of the isolates, with 43% carrying colicin genes and 3% carrying microcin genes. Of the bacteriocins observed (H47, E3, E1, E2, E7, Ia/Ib, and B/M), the frequency with which they were detected varied with respect to gut region for the colicins E2, E7, Ia/Ib, and B/M. The plasmid replicon typing gave rise to 25 profiles from the 13 Inc types detected. Inc F types were detected most frequently, followed by Inc HI1 and N types. Of the Inc types detected, 7 were nonrandomly distributed among isolates from the different regions of the gut. The results of this study indicate that not only may the different regions of the gastrointestinal tract harbor different strains ofE. colibut also that strains from different regions have different characteristics.

scholarly journals Emergence of a Competence-Reducing Filamentous Phage from the Genome of Acinetobacter baylyi ADP1

2016 ◽  
Vol 198 (23) ◽  
pp. 3209-3219 ◽  
Author(s):  
Brian A. Renda ◽  
Cindy Chan ◽  
Kristin N. Parent ◽  
Jeffrey E. Barrick
Keyword(s):  
Acinetobacter Baumannii ◽  
Vibrio Cholerae ◽  
Bacterial Species ◽  
Normal Growth ◽  
Multidrug Resistant ◽  
Filamentous Phage ◽  
Acinetobacter Baylyi ◽  
Laboratory Evolution ◽  
Content Type ◽  
Evolution Experiment

ABSTRACTBacterial genomes commonly contain prophage sequences as a result of past infections with lysogenic phages. Many of these integrated viral sequences are believed to be cryptic, but prophage genes are sometimes coopted by the host, and some prophages may be reactivated to form infectious particles when cells are stressed or mutate. We found that a previously uncharacterized filamentous phage emerged from the genome ofAcinetobacter baylyiADP1 during a laboratory evolution experiment. This phage has a genetic organization similar to that of theVibrio choleraeCTXϕ phage. The emergence of the ADP1 phage was associated with the evolution of reduced transformability in our experimental populations, so we named it thecompetence-reducingacinetobacter phage (CRAϕ). Knocking out ADP1 genes required for competence leads to resistance to CRAϕ infection. Although filamentous bacteriophages are known to target type IV pili, this is the first report of a phage that apparently uses a competence pilus as a receptor.A. baylyimay be especially susceptible to this route of infection because every cell is competent during normal growth, whereas competence is induced only under certain environmental conditions or in a subpopulation of cells in other bacterial species. It is possible that CRAϕ-like phages restrict horizontal gene transfer in nature by inhibiting the growth of naturally transformable strains. We also found that prophages with homology to CRAϕ exist in several strains ofAcinetobacter baumannii. These CRAϕ-likeA. baumanniiprophages encode toxins similar to CTXϕ that might contribute to the virulence of this opportunistic multidrug-resistant pathogen.IMPORTANCEWe observed the emergence of a novel filamentous phage (CRAϕ) from the genome ofAcinetobacter baylyiADP1 during a long-term laboratory evolution experiment. CRAϕ is the first bacteriophage reported to require the molecular machinery involved in the uptake of environmental DNA for infection. Reactivation and evolution of CRAϕ reduced the potential for horizontal transfer of genes via natural transformation in our experiment. Risk of infection by similar phages may limit the expression and maintenance of bacterial competence in nature. The closest studied relative of CRAϕ is theVibrio choleraeCTXϕ phage. Variants of CRAϕ are found in the genomes ofAcinetobacter baumanniistrains, and it is possible that phage-encoded toxins contribute to the virulence of this opportunistic multidrug-resistant pathogen.

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