Experimental Studies of Pleiotropy and Epistasis in Escherichia coli. I. Variation in Competitive Fitness Among Mutants Resistant to Virus T4

Evolution ◽  
1988 ◽  
Vol 42 (3) ◽  
pp. 425 ◽  
Author(s):  
Richard E. Lenski
Keyword(s):  
Escherichia Coli ◽  
Experimental Studies ◽  
Competitive Fitness

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 The Min-protein oscillations in Escherichia coli : an example of self-organized cellular protein waves

2018 ◽  
Vol 373 (1747) ◽  
pp. 20170111 ◽  
Author(s):  
Lukas Wettmann ◽  
Karsten Kruse
Keyword(s):  
Escherichia Coli ◽  
Cell Biology ◽  
Experimental Studies ◽  
Cellular Protein ◽  
Self Organization ◽  
Division Site ◽  
Min Proteins ◽  
Spatio Temporal

In the rod-shaped bacterium Escherichia coli , selection of the cell centre as the division site involves pole-to-pole oscillations of the proteins MinC, MinD and MinE. This spatio-temporal pattern emerges from interactions among the Min proteins and with the cytoplasmic membrane. Combining experimental studies in vivo and in vitro together with theoretical analysis has led to a fairly good understanding of Min-protein self-organization. In different geometries, the system can, in addition to standing waves, also produce travelling planar and spiral waves as well as coexisting stable stationary distributions. Today it stands as one of the best-studied examples of cellular self-organization of proteins. This article is part of the theme issue ‘Self-organization in cell biology’.

scholarly journals Genetic background affects epistatic interactions between two beneficial mutations

2013 ◽  
Vol 9 (1) ◽  
pp. 20120328 ◽  
Author(s):  
Yinhua Wang ◽  
Carolina Díaz Arenas ◽  
Daniel M. Stoebel ◽  
Tim F. Cooper
Keyword(s):  
Escherichia Coli ◽  
Genetic Background ◽  
General Pattern ◽  
Experimental Studies ◽  
Natural Isolate ◽  
Phenotypic Effect ◽  
Fitness Effect ◽  
Epistatic Interactions ◽  
Beneficial Mutations ◽  
E Coli

The phenotypic effect of mutations can depend on their genetic background, a phenomenon known as epistasis. Many experimental studies have found that epistasis is pervasive, and some indicate that it may follow a general pattern dependent on the fitness effect of the interacting mutations. These studies have, however, typically examined the effect of interactions between a small number of focal mutations in a single genetic background. Here, we extend this approach by considering how the interaction between two beneficial mutations that were isolated from a population of laboratory evolved Escherichia coli changes when they are added to divergent natural isolate strains of E. coli . We find that interactions between the focal mutations and the different genetic backgrounds are common. Moreover, the pair-wise interaction between the focal mutations also depended on their genetic background, being more negative in backgrounds with higher absolute fitness. Together, our results indicate the presence of interactions between focal mutations, but also caution that these interactions depend quantitatively on the wider genetic background.

scholarly journals Antimicrobial activity of some plant species used for the medical purpose in Turkey

2017 ◽  
Vol 6 (2) ◽  
pp. 93-97
Author(s):  
Pınar Erecevit ◽  
◽  
Sevda Kırbağ ◽  
Keyword(s):  
Escherichia Coli ◽  
Antimicrobial Activity ◽  
Candida Glabrata ◽  
Experimental Studies ◽  
Antimicrobial Activities ◽  
Disc Diffusion ◽  
Medical Purpose ◽  
Staphylococcus Aureus Cowan ◽  
Rhus Coriaria ◽  
Pistacia Terebinthus

İn this study, the antimicrobial activities of eight species plants, used for treatment of various diseases, were investigated. The extracts of Rhus coriaria L., Pistacia terebinthus L. subsp. palestina, Centaurea virgata Lav., Euphorbia macroclada Boiss., Ceterach officinarum DC., Echinophora tenuifolia L. subsp. sibthorpianal (Guss) Tutin, Equisetum romasissimum Desf., Umbilicus erectus DC. have been prepared with methanol and the antimicrobial activities of these extracts have been examined on test microorganisms as follows: Staphylococcus aureus COWAN 1, Bacillus megaterium DSM 32, Klebsiella pneumoniae FMC 5, Escherichia coli ATCC 25922, Candida albicans FMC 17, Candida glabrata ATCC 66032, C. tropicalis ATCC 13803, Trichophyton sp. and Epidermophyton sp. by disc diffusion methods. The MIC values of plant extracts were determined acording to the microdilutions assays. Results from obtained experimental studies showed that the extracts of R. coriaria, P. terebinthus sub. sp. palestina, U. erectus and C. virgata have been inhibited the growth of all over the microorganisms used in the test at different ratio. But the extracts of E. macroclada, C. officinarum, E. tenuifolia, L. sibthorpianal, E. romasissimum had no effect against some bacteria, yeasts and dermatophyta used in study. Also, The MIC values of real extracts have been determined as 20 - 0.3125 mg/ml.

scholarly journals SoluProt: Prediction of Soluble Protein Expression in Escherichia coli

2020 ◽  
Author(s):  
Jiri Hon ◽  
Martin Marusiak ◽  
Tomas Martinek ◽  
Antonin Kunka ◽  
Jaroslav Zendulka ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Protein Expression ◽  
Soluble Protein ◽  
Experimental Studies ◽  
Computational Prediction ◽  
Supplementary Information ◽  
Gradient Boosting ◽  
Sequence Information ◽  
Success Rates ◽  
Solubility Prediction

<p><b>Motivation:</b> Poor protein solubility hinders the production of many therapeutic and industrially useful proteins. Experimental efforts to increase solubility are plagued by low success rates and often reduce biological activity. Computational prediction of protein expressibility and solubility in <i>Escherichia coli</i> using only sequence information could reduce the cost of experimental studies by enabling prioritisation of highly soluble proteins.</p> <p><b>Results:</b> A new tool for sequence-based prediction of soluble protein expression in <i>Escherichia coli, </i>SoluProt, was created using the gradient boosting machine technique with the TargetTrack database as a training set. When evaluated against a balanced independent test set derived from the NESG database, SoluProt’s accuracy of 58.4% and AUC of 0.60 exceeded those of a suite of alternative solubility prediction tools. There is also evidence that it could significantly increase the success rate of experimental protein studies. SoluProt is freely available as a standalone program and a user-friendly webserver at <a href="https://loschmidt.chemi.muni.cz/soluprot/">https://loschmidt.chemi.muni.cz/soluprot/</a>.</p> <p> </p> <p>Availability and Implementation: <a href="https://loschmidt.chemi.muni.cz/soluprot/">https://loschmidt.chemi.muni.cz/soluprot/</a></p> <p>Contact: [email protected]</p> Supplementary Information: Supplementary data are available at Bioinformatics online

scholarly journals SoluProt: Prediction of Soluble Protein Expression in Escherichia coli

2020 ◽  
Author(s):  
Jiri Hon ◽  
Martin Marusiak ◽  
Tomas Martinek ◽  
Antonin Kunka ◽  
Jaroslav Zendulka ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Protein Expression ◽  
Soluble Protein ◽  
Experimental Studies ◽  
Computational Prediction ◽  
Supplementary Information ◽  
Gradient Boosting ◽  
Sequence Information ◽  
Success Rates ◽  
Solubility Prediction

<p><b>Motivation:</b> Poor protein solubility hinders the production of many therapeutic and industrially useful proteins. Experimental efforts to increase solubility are plagued by low success rates and often reduce biological activity. Computational prediction of protein expressibility and solubility in <i>Escherichia coli</i> using only sequence information could reduce the cost of experimental studies by enabling prioritisation of highly soluble proteins.</p> <p><b>Results:</b> A new tool for sequence-based prediction of soluble protein expression in <i>Escherichia coli, </i>SoluProt, was created using the gradient boosting machine technique with the TargetTrack database as a training set. When evaluated against a balanced independent test set derived from the NESG database, SoluProt’s accuracy of 58.4% and AUC of 0.60 exceeded those of a suite of alternative solubility prediction tools. There is also evidence that it could significantly increase the success rate of experimental protein studies. SoluProt is freely available as a standalone program and a user-friendly webserver at <a href="https://loschmidt.chemi.muni.cz/soluprot/">https://loschmidt.chemi.muni.cz/soluprot/</a>.</p> <p> </p> <p>Availability and Implementation: <a href="https://loschmidt.chemi.muni.cz/soluprot/">https://loschmidt.chemi.muni.cz/soluprot/</a></p> <p>Contact: [email protected]</p> Supplementary Information: Supplementary data are available at Bioinformatics online

scholarly journals Mutations that improve efficiency of a weak-link enzyme are rare compared to adaptive mutations elsewhere in the genome

eLife ◽  
2019 ◽  
Vol 8 ◽  
Author(s):  
Andrew B Morgenthaler ◽  
Wallis R Kinney ◽  
Christopher C Ebmeier ◽  
Corinne M Walsh ◽  
Daniel J Snyder ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Metabolic Pathway ◽  
Weak Link ◽  
Experimental Studies ◽  
Wild Type ◽  
Gene Encoding ◽  
Evolutionary Trajectory ◽  
Adaptive Mutations ◽  
E Coli ◽  
Essential Function

New enzymes often evolve by gene amplification and divergence. Previous experimental studies have followed the evolutionary trajectory of an amplified gene, but have not considered mutations elsewhere in the genome when fitness is limited by an evolving gene. We have evolved a strain of Escherichia coli in which a secondary promiscuous activity has been recruited to serve an essential function. The gene encoding the ‘weak-link’ enzyme amplified in all eight populations, but mutations improving the newly needed activity occurred in only one. Most adaptive mutations occurred elsewhere in the genome. Some mutations increase expression of the enzyme upstream of the weak-link enzyme, pushing material through the dysfunctional metabolic pathway. Others enhance production of a co-substrate for a downstream enzyme, thereby pulling material through the pathway. Most of these latter mutations are detrimental in wild-type E. coli, and thus would require reversion or compensation once a sufficient new activity has evolved.

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