Growth of E. coli on lactate as a carbon source leads to altered phenotypes, specifically decreased acetate overflow, which serves to tune cellular energy metabolism.
Goodarzi H, Bennett B, Amini S, Reaves M, Hottes A, Rabinowitz J, and Tavazoie S (2010) analyzed regulatory and metabolic rewiring during laboratory evolution of ethanol tolerance in Escherichia coli, published in Molecular Systems Biology.
Increased growth in Escherichia coli during osmotic stress is linked to mutations that lead to increased expression of enterobactin biosynthesis genes, including fepA and entD.
The rpoC mutations identified in Escherichia coli during glycerol growth selection led to altered gene expression patterns by globally redistributing transcriptional units from ribosomal RNAs to other units.
Increased ethanol tolerance in Escherichia coli can be mediated by increased catabolism of ethanol through the TCA cycle.
T. Cooper and R. Lenski published the paper 'Experimental evolution with E. coli in diverse resource environments. I. Fluctuating environments promote divergence of replicate populations' in the journal BMC Evolutionary Biology in 2010 (Volume 10, article 11).
Experimental Escherichia coli cultures have demonstrated the ability to evolve novel traits on a laboratory time scale, such as the aerobic utilization of citrate, the ability to use the non-natural carbon source 1,2-propanediol, and the development of compensatory mutations to restore glutathione biosynthesis in a deficient strain.
Sleight S, Orlic C, Schneider D, and Lenski R (2008) investigated the genetic basis of evolutionary adaptation by Escherichia coli to stressful cycles of freezing, thawing, and growth, published in Genetics.
Pelosi et al. (2006) published 'Parallel changes in global protein profiles during long-term experimental evolution in Escherichia coli' in Genetics, volume 173, pages 1851-1869.
Escherichia coli populations with an rpoS deletion can develop increased salt tolerance during laboratory evolution by uncoupling the rpoS-dependent expression of the otsBA operon, which is necessary for trehalose synthesis.
Philippe N, Crozat E, Lenski R, and Schneider D studied the evolution of global regulatory networks in Escherichia coli during a long-term experiment, as published in BioEssays in 2007.
Crozat et al. (2010) published 'Parallel genetic and phenotypic evolution of DNA superhelicity in experimental populations of Escherichia coli' in Molecular Biology and Evolution, volume 27, pages 2113-2128.
In typical E. coli or S. cerevisiae cultures, a fitness increase of 50–100% can be achieved within 100 to 500 generations, which corresponds to approximately 2 months of selection.
Escherichia coli populations exposed to prolonged increased temperature show adaptive expression changes in heat-inducible genes, specifically hslT, fkpA, and gapA.
Minty JJ, Lesnefsky AA, Lin F, Chen Y, Zaroff TA, Veloso AB, Xie B, McConnell CA, Ward RJ, and Schwartz DR (2011) combined evolution and genomic study to elucidate the genetic bases of isobutanol tolerance in Escherichia coli, published in Microbial Cell Factories.
In a study on Escherichia coli batch selection for growth on glycerol, rpoC RNA polymerase mutations were identified as a major source for improved growth, leading to a biomass yield increase of up to 40%, reduced acetate overflow, increased metabolic rate, and a lowered or total loss of motility.
Paul Sniegowski, Paul Gerrish, and Richard Lenski demonstrated the evolution of high mutation rates in experimental populations of Escherichia coli in a 1997 study published in Nature.
Jeffrey Barrick, D. Yu, S. Yoon, H. Jeong, T. Oh, D. Schneider, Richard Lenski, and J. Kim analyzed genome evolution and adaptation in a long-term experiment with Escherichia coli in a 2009 study published in Nature.
Adaptive evolution towards increased iso- and n-butanol stress in Escherichia coli involves mutations in acrAB and marC, as well as changes in carbon and nitrogen metabolism via gatY and tnaA, enterobactin synthesis, and attenuated rpoS activity via hfq mutations.
In a single Escherichia coli population grown under glycerol-limited conditions, one stable mutant showed increased growth in glycerol-sufficient batch cultures, while a second mutant did not; the mutant with increased growth in batch culture also exhibited increased fitness under general nutrient limitation, heat stress, and osmotic stress.
Richard Lenski, J. Mongold, Paul Sniegowski, M. Travisano, F. Vasi, Paul Gerrish, and T. Schmidt investigated the evolution of competitive fitness in experimental populations of Escherichia coli in a 1998 study published in Antonie van Leeuwenhoek.
In the last 25 years, there has been an increasing number of adaptive laboratory evolution experiments, with Escherichia coli and Saccharomyces cerevisiae being the most prominent organisms under investigation.
Phosphate limitation experiments caused genotypic and phenotypic divergence in E. coli through mutations in the rpoS, spoT, and hfq genes, which led to the de-regulation of pho genes and increased phosphate transport.
The SPANC balance (self-preservation and nutritional competence) in Escherichia coli is governed by strict control of processes such as stress and stringent responses.
Vaughn Cooper and Richard Lenski studied the population genetics of ecological specialization in evolving Escherichia coli populations in a 2000 paper published in Nature.
In Escherichia coli, increased ethanol tolerance results in decreased resistance to acidic conditions.
Adaptive changes towards ethanol tolerance in Escherichia coli are linked to the up-regulation of oxyR and nrdR, which indicates major changes in the cellular respiratory system and amino acid metabolism.
Sleight S and Lenski R (2007) examined evolutionary adaptation to freeze-thaw-growth cycles in Escherichia coli, published in Physiological and Biochemical Zoology.
In a study of Escherichia coli, a mutator phenotype (mutT) was invaded by mutY mutations, where the mutT mutation led to an approximately 150-fold increase in the mutation rate, while the mutY mutations decreased the mutation rate by 40–60% to reduce genetic load.
Feist et al. (2010) performed a model-driven evaluation of the production potential for growth-coupled products of Escherichia coli.
Adaptation to extreme temperature in Escherichia coli relies on the constitutive expression of GroEL/ES.
Notley-McRobb and Ferenci (1999) observed the generation of multiple co-existing mal-regulatory mutations through polygenic evolution in glucose-limited populations of Escherichia coli.
In E. coli, lacZ expression levels were evolutionarily fine-tuned depending on the lactose concentration in the environment to balance the cost of lacZ expression and increased fitness.
Hughes, Cullum, and Bennett (2007) studied evolutionary adaptation to environmental pH in experimental lineages of Escherichia coli.
Chen T, Wang J, Yang R, Li J, Lin M, and Lin Z showed that laboratory-evolved mutants of the exogenous global regulator IrrE from Deinococcus radiodurans enhance the stress tolerances of Escherichia coli in a 2011 study published in PLoS One.
In Escherichia coli, n-butanol tolerance is weakly compatible with oxidative stress and leads to trade-offs in hexane and chloramphenicol resistance.
P. Charusanti, T.M. Conrad, E.M. Knight, K. Venkataraman, N.L. Fong, B. Xie, Y. Gao, and B. Palsson published the paper 'Genetic basis of growth adaptation of Escherichia coli after deletion of pgi, a major metabolic gene' in the journal PLoS Genetics in 2010 (Volume 6, article e1001186).
M. Dragosits, V. Mozhayskiy, S. Quinones-Soto, J. Park, and I. Tagkopoulos published the paper 'Evolutionary potential, cross-stress behavior and the genetic basis of acquired stress resistance in Escherichia coli' in the journal Molecular Systems Biology in 2013 (Volume 9, article 643).
Reyes et al. (2012) visualized evolution in real time to determine the molecular mechanisms of n-butanol tolerance in Escherichia coli, published in Metabolic Engineering.
Notley-McRobb L, Pinto R, Seeto S, and Ferenci T published 'Regulation of mutY and nature of mutator mutations in Escherichia coli populations under nutrient limitation' in the Journal of Bacteriology in 2002.
Mesophilic organisms such as Escherichia coli and Saccharomyces cerevisiae have inherent properties that limit their use in high-temperature processes, necessitating the use of non-conventional microbial species in biotechnology.
Long-term batch cultivation of Escherichia coli on glucose leads to a rapid decay of non-used metabolic functions, specifically the ability to grow on D-ribose and L-glutamine.
S. Fong, A. Joyce, and B. Palsson published the paper 'Parallel adaptive evolution cultures of Escherichia coli lead to convergent growth phenotypes with different gene expression states' in the journal Genome Research in 2005 (Volume 15, pages 1365-1372).
In a 1997 study, Escherichia coli was evolved in chemostat cultures to select for improved growth on glycerol, resulting in phenotypic changes including altered colony morphology, increased growth rate, increased biomass yield, and decreased acetate formation.
Researchers introduced a heterologous transcriptional regulator from Deinococcus radiodurans into Escherichia coli to select for improved phenotypes, demonstrating that extensive perturbations of regulatory networks can expand possibilities in rapid laboratory evolution towards complex traits.
Orth JD, Conrad TM, Na J, Lerman JA, Nam H, Feist AM, and Palsson B published a comprehensive genome-scale reconstruction of Escherichia coli metabolism in 2011 in Molecular Systems Biology.
Silver and Mateles (1969) studied the control of mixed-substrate utilization in continuous cultures of Escherichia coli in the Journal of Bacteriology.
Researchers achieved a drastic increase in n-butanol tolerance in Escherichia coli by combining laboratory evolution with genome shuffling of the evolved clones.
In Escherichia coli, evolutionarily 'old' anticipatory responses can be rapidly decoupled by using increased genotypic diversity leveraged by a transposon library.
Weikert, Sauer, and Bailey (1997) utilized a glycerol-limited, long-term chemostat to isolate Escherichia coli mutants with improved physiological properties.
Multiplexed automated genome engineering (MAGE) technology utilizes massively increased genotypic diversity to generate improved phenotypes, such as improved lycopene production in Escherichia coli, and to accelerate evolution.
Lederberg (1951) reported on the prevalence of Escherichia coli strains exhibiting genetic recombination in the journal Science.
Mutations in amino acid catabolic processes and the stress response sigma factor, rpoS, are critical for acquiring a selective advantage in nutrient-starved conditions for Escherichia coli.
Yeast cells possess an intrinsic sensing mechanism similar to the SPANC balance in Escherichia coli, which allows them to balance growth and stress resistance.
Increased oxidative stress resistance in Escherichia coli may be linked to mutations in the soxR reducing system and increased levels of cellular catalase/peroxidase (katG).
Zambrano et al. (1993) identified Escherichia coli mutants that take over stationary phase cultures, demonstrating microbial competition.
General evolutionary principles observed in Escherichia coli and Saccharomyces cerevisiae, such as the tendency toward optimized biomass yield, overflow metabolism, large-scale regulatory changes, and the emergence of mutator strains, also occur in other microbial hosts like Lactococcus lactis.
Researchers applied laboratory evolution to recombinant E. coli through serial transfers to improve anaerobic growth on xylose, aiming to allow homofermentative L-lactic acid production.
T.M. Conrad, M. Frazier, A.R. Joyce, B.K. Cho, E.M. Knight, N.E. Lewis, R. Landick, and B. Palsson published the paper 'RNA polymerase mutants found through adaptive evolution reprogram Escherichia coli for optimal growth in minimal media' in the journal Proceedings of the National Academy of Sciences USA in 2010 (Volume 107, pages 20500-20505).
GASP (growth advantage in stationary phase) mutants are rapidly fixed in Escherichia coli populations.
Q. Hua, A.R. Joyce, B. Palsson, and S.S. Fong published the paper 'Metabolic characterization of Escherichia coli strains adapted to growth on lactate' in the journal Applied and Environmental Microbiology in 2007 (Volume 73, pages 4639-4647).
Riehle M, Bennett A, Lenski R, and Long A (2003) analyzed evolutionary changes in heat-inducible gene expression in lines of Escherichia coli adapted to high temperature, published in Physiological Genomics.
The occurrence of enterobactin-related mutations in multiple adaptive laboratory evolution studies highlights the importance of tuning the cellular redox machinery during environmental stress exposure in Escherichia coli.
Manch, Notley-McRobb, and Ferenci (1999) found that the mutational adaptation of Escherichia coli to glucose limitation involves distinct evolutionary pathways in aerobic versus oxygen-limited environments.
L. Wang, B. Spira, Z. Zhou, L. Feng, R.P. Maharjan, X. Li, F. Li, C. McKenzie, P.R. Reeves, and T. Ferenci observed divergence involving global regulatory gene mutations in an Escherichia coli population evolving under phosphate limitation in a 2010 study published in Genome Biology and Evolution.
Approximately 30% of genes in well-studied organisms such as Escherichia coli and Saccharomyces cerevisiae have unknown functions.
Mutations in E. coli resulted in a reduced diauxic lag phase and increased maximum growth rates when the bacteria were grown in a lactose growth medium.
Rudolph B, Gebendorfer KM, Buchner J, and Winter J (2010) studied the evolution of Escherichia coli for growth at high temperatures, published in the Journal of Biological Chemistry.
Atsumi S, Wu TY, Machado IM, Huang WC, Chen PY, Pellegrini M, and Liao JC (2010) studied the evolution, genomic analysis, and reconstruction of isobutanol tolerance in Escherichia coli, published in Molecular Systems Biology.
Mutations identified in isobutanol-resistant Escherichia coli strains show a high degree of epistasis.
R.J. Woods, Jeffrey Barrick, T.F. Cooper, U. Shrestha, M.R. Kauth, and Richard Lenski provided evidence for second-order selection for evolvability in a large Escherichia coli population in a 2011 study published in Science.
Lee DH, Feist AM, Barrett CL, and Palsson B published 'Cumulative number of cell divisions as a meaningful timescale for adaptive laboratory evolution of Escherichia coli' in the Journal of General Microbiology in 1980.
E. coli can evolve different modes of lacZ expression depending on whether the environment contains lactose, glucose, or both as carbon sources, with mutations accumulating predominantly in the lacI and lacO1 regions of the lac operon.
Liu M, Durfee T, Cabrera J, Zhao K, Jin D, and Blattner F revealed a carbon source foraging strategy by Escherichia coli through global transcriptional programs, published in J Biol Chem in 2005.
Quan S, Ray JC, Kwota Z, Duong T, Balázsi G, Cooper TF, and Monds RD (2012) investigated the adaptive evolution of the lactose utilization network in experimentally evolved populations of Escherichia coli, published in PLoS Genetics.
T. Cooper, D. Rozen, and R. Lenski published the paper 'Parallel changes in gene expression after 20,000 generations of evolution in Escherichia coli' in the journal Proceedings of the National Academy of Sciences USA in 2003 (Volume 100, pages 1072-1077).
Independent studies have observed changes in enterobactin biosynthetic processes (ent genes) in Escherichia coli during adaptive evolution experiments.
Professor Lenski and his research group at Michigan State University have conducted a long-term adaptive laboratory evolution study using Escherichia coli that has exceeded 50,000 generations.
Alcántara-Díaz D, Breña-Valle M, and Serment-Guerrero J (2004) studied the divergent adaptation of Escherichia coli to cyclic ultraviolet light exposures, published in Mutagenesis.
Adaptation to extreme temperature in Escherichia coli can be achieved through mutations in glpF and fabA, which are accompanied by increased membrane fatty acid saturation.
Horinouchi T, Tamaoka K, Furusawa C, Ono N, Suzuki S, Hirasawa T, Yomo T, and Shimizu H (2010) performed a transcriptome analysis of parallel-evolved Escherichia coli strains under ethanol stress, published in BMC Genomics.
Stoebel D, Hokamp K, Last M, and Dorman C (2009) studied the compensatory evolution of gene regulation in response to stress by Escherichia coli lacking RpoS, published in PLoS Genetics.
Notley-McRobb L, Seeto S, and Ferenci T published 'Enrichment and elimination of mutY mutators in Escherichia coli populations' in Genetics in 2002.
Low-temperature evolved Escherichia coli populations do not universally exhibit trade-offs at high temperatures, as individual lineages may show no trade-offs or even increased fitness.
Zachary Blount, C. Borland, and Richard Lenski examined historical contingency and the evolution of a key innovation in an experimental population of Escherichia coli in a 2008 study published in the Proceedings of the National Academy of Sciences (PNAS).