scholarly journals Local adaptation mediated niche expansion in correlation with genetic richness

2021 ◽  
Author(s):  
Masaomi Kurokawa ◽  
Issei Nishimura ◽  
Bei-Wen YING
Keyword(s):  
Escherichia Coli ◽  
Local Adaptation ◽  
High Throughput ◽  
Experimental Evolution ◽  
Environmental Gradient ◽  
Growth Curves ◽  
Quantitative Relationship ◽  
Central Issue ◽  
Wild Type ◽  
Niche Expansion

As a central issue in evolution and ecology, the quantitative relationship among the genome, adaptation and the niche was investigated. Local adaptation of five Escherichia coli strains carrying either the wild-type genome or reduced genomes was achieved by experimental evolution. A high-throughput fitness assay of the ancestor and evolved populations across an environmental gradient of eight niches resulted in a total of 80 fitness curves generated from 2,220 growth curves. Further analyses showed that the increases in both local adaptiveness and niche broadness were negatively correlated with genetic richness. Local adaptation caused common niche expansion, whereas niche expansion for generality or speciality was decided by genetic richness. The order of the mutations accumulated stepwise was correlated with the magnitude of the fitness increase attributed to mutation accumulation. Pre-adaptation probably participated in coordination among genetic richness, local adaptation and niche expansion.

scholarly journals Local adaptation mediated niche expansion in correlation with genetic richness

2021 ◽  
Author(s):  
Masaomi Kurokawa ◽  
Issei Nishimura ◽  
Bei-Wen Ying
Keyword(s):  
Escherichia Coli ◽  
Local Adaptation ◽  
High Throughput ◽  
Experimental Evolution ◽  
Environmental Gradient ◽  
Growth Curves ◽  
Quantitative Relationship ◽  
Central Issue ◽  
Wild Type ◽  
Niche Expansion

Abstract As a central issue in evolution and ecology, the quantitative relationship among the genome, adaptation and the niche was investigated. Local adaptation of five Escherichia coli strains carrying either the wild-type genome or reduced genomes was achieved by experimental evolution. A high-throughput fitness assay of the ancestor and evolved populations across an environmental gradient of eight niches resulted in a total of 80 fitness curves generated from 2,220 growth curves. Further analyses showed that the increases in both local adaptiveness and niche broadness were negatively correlated with genetic richness. Local adaptation caused common niche expansion, whereas niche expansion for generality or speciality was decided by genetic richness. The order of the mutations accumulated stepwise was correlated with the magnitude of the fitness increase attributed to mutation accumulation. Pre-adaptation probably participated in coordination among genetic richness, local adaptation and niche expansion.

scholarly journals The Consequences of Growth of a Mutator Strain of Escherichia coli as Measured by Loss of Function Among Multiple Gene Targets and Loss of Fitness

Genetics ◽  
2000 ◽  
Vol 154 (3) ◽  
pp. 959-970 ◽  
Author(s):  
Pauline Funchain ◽  
Annie Yeung ◽  
Jean Lee Stewart ◽  
Rose Lin ◽  
Malgorzata M Slupska ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Mismatch Repair ◽  
Growth Curves ◽  
Temperature Sensitive ◽  
Loss Of Function ◽  
Wild Type ◽  
Average Cell ◽  
Mutator Strain ◽  
Single Colony ◽  
Intergenic Regions

Abstract We have examined the composition of members of mutator populations of Escherichia coli by employing an extensive set of phenotypic screens that allow us to monitor the function of >700 genes, constituting ~15% of the genome. We looked at mismatch repair deficient cells after repeated cycles of single colony isolation on rich medium to generate lineages that are forced through severe bottlenecks, and compared the results to those for wild-type strains. The mutator lineages continued to accumulate mutations rapidly with each increasing cycle of colony isolation. By the end of the 40th cycle, after ~1000 generations, most of the lineages had reduced colony size, 4% had died out, 55% had auxotrophic requirements (increasing to 80% after 60 cycles), and 70% had defects in at least one sugar or catabolic pathway. In addition, 33% had a defect in cell motility, and 26% were either temperature-sensitive or cold-sensitive lethals. On the other hand, only 3% of the wild-type lineages had detectable mutations of any type after 40 cycles. By the 60th cycle, the typical mutator cell carried 4–5 inactive genes among the 15% of the genome being monitored, indicating that the average cell carried at least 24–30 inactivated genes distributed throughout the genome. Remarkably, 30% of the lineages had lost the ability to utilize xylose as a carbon source. DNA sequencing revealed that most of the Xyl− mutants had a frameshift in a run of eight G's (GGGGGGGG) in the xylB gene, either adding or deleting one -G-. Further analysis indicated that rendering E. coli deficient in mismatch repair unmasks hypermutable sites in certain genes or intergenic regions. Growth curves and competition tests on lineages that passed through 90 cycles of single colony isolation showed that all lineages suffered reduced fitness. We discuss these results in terms of the value of mutators in cellular evolution.

scholarly journals The effect of spatial structure on adaptation in Escherichia coli

2007 ◽  
Vol 4 (1) ◽  
pp. 57-59 ◽  
Author(s):  
Lilia Perfeito ◽  
M. Inês Pereira ◽  
Paulo R.A Campos ◽  
Isabel Gordo
Keyword(s):  
Escherichia Coli ◽  
Spatial Structure ◽  
Experimental Evolution ◽  
Petri Dish ◽  
Mutation Rates ◽  
Wild Type ◽  
Clonal Interference ◽  
Genetic Studies ◽  
Significant Difference ◽  
The Cost

Populations of organisms are generally organized in a given spatial structure. However, the vast majority of population genetic studies are based on populations in which every individual competes globally. Here we use experimental evolution in Escherichia coli to directly test a recently made prediction that spatial structure slows down adaptation and that this cost increases with the mutation rate. This was studied by comparing populations of different mutation rates adapting to a liquid (unstructured) medium with populations that evolved in a Petri dish on solid (structured) medium. We find that mutators adapt faster to both environments and that adaptation is slower if there is spatial structure. We observed no significant difference in the cost of structure between mutator and wild-type populations, which suggests that clonal interference is intense in both genetic backgrounds.

scholarly journals Larger increases in sensitivity to paracatalytic inactivation than in catalytic competence during experimental evolution of the second β-galactosidase of Escherichia coli

1997 ◽  
Vol 325 (1) ◽  
pp. 117-121 ◽  
Author(s):  
Sergei V. CALUGARU ◽  
Srinivasan KRISHNAN ◽  
Calvin J. CHANY ◽  
Barry G. HALL ◽  
Michael L. SINNOTT
Keyword(s):  
Escherichia Coli ◽  
Rate Constants ◽  
Experimental Evolution ◽  
First Generation ◽  
Bacterial Resistance ◽  
Enzyme Inactivation ◽  
Third Generation ◽  
Wild Type ◽  
Lower Effect ◽  
Partial Inactivation

Second-order rate constants (M-1·s-1) at 25 °C and pH 7.5 for inactivation of first-generation (ebga and ebgb), second-generation(ebgab and ebgabcd) and third-generation (ebgabcde) experimental evolvants of the title enzyme by 2′,4′-dinitrophenyl 2-deoxy-2-fluoro-β-d-galactopyranoside are 0.042, 0.30, 10, 24 and 57 respectively. Only partial inactivation is observed, except forebgabcde. At a single high inactivator concentration, inactivation of the wild-type ebgo is also seen. The changes in sensitivity to the paracatalytic inactivator (over a range of 103.3) are larger than changes in kcat/Km for lactose (over a range of 102.7) or nitrophenyl galactosides (over a range of only 101.3), or changes in degalactosylation rate (over a range of 101.7). These data raise the possibility that evolution in the reverse sense, towards insensitivity to a paracatalytic inactivator with a proportionally lower effect on transformation of substrate, may become a mechanism for the development of bacterial resistance to antibiotics that act by paracatalytic enzyme inactivation.

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.

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