scholarly journals Long-Term Experimental Evolution in Escherichia coli. IV. Targets of Selection and the Specificity of Adaptation

Genetics ◽  
1996 ◽  
Vol 143 (1) ◽  
pp. 15-26 ◽  
Author(s):  
Michael Travisano ◽  
Richard E Lenski
Keyword(s):  
Escherichia Coli ◽  
Experimental Evolution ◽  
Common Ancestor ◽  
The Novel ◽  
Physiological Mechanisms ◽  
Outer Membranes ◽  
Limiting Nutrient ◽  
Novel Environments ◽  
Uptake Mechanisms

Abstract This study investigates the physiological manifestation of adaptive evolutionary change in 12 replicate populations of Escherichia coli that were propagated for 2000 generations in a glucose-limited environment. Representative genotypes from each population were assayed for fitness relative to their common ancestor in the experimental glucose environment and in 11 novel single-nutrient environments. After 2000 generations, the 12 derived genotypes had diverged into at least six distinct phenotypic classes. The nutrients were classified into four groups based upon their uptake physiology. All 12 derived genotypes improved in fitness by similar amounts in the glucose environment, and this pattern of parallel fitness gains was also seen in those novel environments where the limiting nutrient shared uptake mechanisms with glucose. Fitness showed little or no consistent improvement, but much greater genetic variation, in novel environments where the limiting nutrient differed from glucose in its uptake mechanisms. This pattern of fitness variation in the novel nutrient environments suggests that the independently derived genotypes adapted to the glucose environment by similar, but not identical, changes in the physiological mechanisms for moving glucose across both the inner and outer membranes.

scholarly journals Long-Term Experimental Evolution in Escherichia coli. VI. Environmental Constraints on Adaptation and Divergence

Genetics ◽  
1997 ◽  
Vol 146 (2) ◽  
pp. 471-479 ◽  
Author(s):  
Michael Travisano
Keyword(s):  
Escherichia Coli ◽  
Genetic Variation ◽  
Experimental Evolution ◽  
Population Genetic ◽  
Environmental Constraints ◽  
Asymmetric Pattern ◽  
Nutrient Environment ◽  
Mean Fitness ◽  
Population Genetic Variation

The effect of environment on adaptation and divergence was examined in two sets of populations of Escherichia coli selected for 1000 generations in either maltose- or glucose-limited media. Twelve replicate populations selected in maltose-limited medium improved in fitness in the selected environment, by an average of 22.5%. Statistically significant among-population genetic variation for fitness was observed during the course of the propagation, but this variation was small relative to the fitness improvement. Mean fitness in a novel nutrient environment, glucose-limited medium, improved to the same extent as in the selected environment, with no statistically significant among-population genetic variation. In contrast, 12 replicate populations previously selected for 1000 generations in glucose-limited medium showed no improvement, as a group, in fitness in maltose-limited medium and substantial genetic variation. This asymmetric pattern of correlated responses suggests that small changes in the environment can have profound effects on adaptation and divergence.

scholarly journals Escherichia coli has a Unique Transcriptional Program in Long-Term Stationary Phase

2020 ◽  
Author(s):  
Karin E. Kram ◽  
Autumn Henderson ◽  
Steven E. Finkel
Keyword(s):  
Escherichia Coli ◽  
Stationary Phase ◽  
Experimental Evolution ◽  
Model Systems ◽  
Natural Environments ◽  
Complex Environments ◽  
Transcriptional Program ◽  
Complex Environment ◽  
Stressful Environment

AbstractMicrobes live in complex and consistently changing environments, but it is difficult to replicate this in the laboratory. Escherichia coli has been used as a model organism in experimental evolution studies for years; specifically, we and others have used it to study evolution in complex environments by incubating the cells into long-term stationary phase (LTSP) in rich media. In LTSP, cells experience a variety of stresses and changing conditions. While we have hypothesized that this experimental system is more similar to natural environments than some other lab conditions, we do not yet know how cells respond to this environment biochemically or physiologically. In this study, we begin to unravel the cells’ responses to this environment by characterizing the transcriptome of cells during LTSP. We found that cells in LTSP have a unique transcriptional program, and that several genes are uniquely upregulated or downregulated in this phase. Further, we identified two genes, cspB and cspI, which are most highly expressed in LTSP, even though these genes are primarily known to respond to cold-shock. When competed with wild-type cells, these genes are also important for survival during LTSP. These data allow us to compare biochemical responses to multiple environments and identify useful model systems, identify gene products that may play a role in survival in this complex environment, and identify novel functions of proteins.ImportanceExperimental evolution studies have elucidated evolutionary processes, but usually in chemically well-defined and/or constant environments. Using complex environments is important to begin to understand how evolution may occur in natural environments, such as soils or within a host. However, characterizing the stresses cells experience in these complex environments can be challenging. One way to approach this is by determining how cells biochemically acclimate to heterogenous environments. In this study we begin to characterize physiological changes by analyzing the transcriptome of cells in a dynamic complex environment. By characterizing the transcriptional profile of cells in long-term stationary phase, a heterogenous and stressful environment, we can begin to understand how cells physiologically and biochemically react to the laboratory environment, and how this compares to more natural conditions.

Long-Term Experimental Evolution in Escherichia coli. IX. Characterization of Insertion Sequence-Mediated Mutations and Rearrangements

Genetics ◽  
2000 ◽  
Vol 156 (2) ◽  
pp. 477-488
Author(s):  
Dominique Schneider ◽  
Esther Duperchy ◽  
Evelyne Coursange ◽  
Richard E Lenski ◽  
Michel Blot
Keyword(s):  
Escherichia Coli ◽  
Experimental Evolution ◽  
Insertion Sequence ◽  
Term Evolution ◽  
Molecular Events ◽  
Evolution Experiment ◽  
Two Populations ◽  
Escherichia Coli B

Abstract As part of a long-term evolution experiment, two populations of Escherichia coli B adapted to a glucose minimal medium for 10,000 generations. In both populations, multiple IS-associated mutations arose that then went to fixation. We identify the affected genetic loci and characterize the molecular events that produced nine of these mutations. All nine were IS-mediated events, including simple insertions as well as recombination between homologous elements that generated inversions and deletions. Sequencing DNA adjacent to the insertions indicates that the affected genes are involved in central metabolism (knockouts of pykF and nadR), cell wall synthesis (adjacent to the promoter of pbpA-rodA), and ill-defined functions (knockouts of hokB-sokB and yfcU). These genes are candidates for manipulation and competition experiments to determine whether the mutations were beneficial or merely hitchhiked to fixation.

scholarly journals Escherichia coli Has a Unique Transcriptional Program in Long-Term Stationary Phase Allowing Identification of Genes Important for Survival

mSystems ◽  
2020 ◽  
Vol 5 (4) ◽  
Author(s):  
Karin E. Kram ◽  
Autumn L. Henderson ◽  
Steven E. Finkel
Keyword(s):  
Escherichia Coli ◽  
Stationary Phase ◽  
Experimental Evolution ◽  
Natural Environments ◽  
Complex Environments ◽  
Transcriptional Program ◽  
Complex Environment ◽  
Content Type ◽  
Stressful Environment

ABSTRACT Microbes live in complex and constantly changing environments, but it is difficult to replicate this in the laboratory. Escherichia coli has been used as a model organism in experimental evolution studies for years; specifically, we and others have used it to study evolution in complex environments by incubating the cells into long-term stationary phase (LTSP) in rich media. In LTSP, cells experience a variety of stresses and changing conditions. While we have hypothesized that this experimental system is more similar to natural environments than some other lab conditions, we do not yet know how cells respond to this environment biochemically or physiologically. In this study, we began to unravel the cells’ responses to this environment by characterizing the transcriptome of cells during LTSP. We found that cells in LTSP have a unique transcriptional program and that several genes are uniquely upregulated or downregulated in this phase. Further, we identified two genes, cspB and cspI, which are most highly expressed in LTSP, even though these genes are primarily known to respond to cold shock. By competing cells lacking these genes with wild-type cells, we show that these genes are also important for survival during LTSP. These data can help identify gene products that may play a role in survival in this complex environment and lead to identification of novel functions of proteins. IMPORTANCE Experimental evolution studies have elucidated evolutionary processes, but usually in chemically well-defined and/or constant environments. Using complex environments is important to begin to understand how evolution may occur in natural environments, such as soils or within a host. However, characterizing the stresses that cells experience in these complex environments can be challenging. One way to approach this is by determining how cells biochemically acclimate to heterogenous environments. In this study, we began to characterize physiological changes by analyzing the transcriptome of cells in a dynamic complex environment. By characterizing the transcriptional profile of cells in long-term stationary phase, a heterogenous and stressful environment, we can begin to understand how cells physiologically and biochemically react to the laboratory environment, and how this compares to more-natural conditions.

scholarly journals Long-term experimental evolution decouples size and production costs in Escherichia coli

2021 ◽  
Author(s):  
Dustin Marshall ◽  
Martino Malerba ◽  
Tom Lines ◽  
Aysha Sezmis ◽  
Chowhury Hasan ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Experimental Evolution ◽  
Strong Support ◽  
Experimental Tests ◽  
Production Costs ◽  
Metabolic Theory ◽  
Metabolic Scaling ◽  
Energy Equivalence ◽  
Costs Of Production

Body size covaries with population dynamics across lifes domains. Theory holds that metabolism imposes fundamental constraints on the coevolution of size and demography. However, studies of interspecific patterns are confounded by other factors that covary with size and demography, and experimental tests of the causal links remain elusive. Here we leverage a 60,000-generation experiment in which Escherichia coli populations evolved larger cells to examine intraspecific metabolic scaling and correlations with demographic parameters. Metabolic theory successfully predicted the relations among size, metabolism, and maximum population density, with strong support for Damuths law of energy equivalence in this experiment. In contrast, populations of larger cells grew faster than those of smaller cells, contradicting the fundamental assumption that costs of production should increase proportionately with size. The finding that the costs of production are substantially decoupled from size requires re-examining the evolutionary drivers and ecological consequences of biological size more generally.

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