Escherichia coli str. K-12 substr. MG1655
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PROVIDER: PRJNA292751 | ENA |
REPOSITORIES: ENA
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Project description:The hypothesis that increased fitness within a selective environment must be accompanied by a loss of fitness in other non-selective environments leads to the notion of evolutionary tradeoffs. Experimental evolution provides an approach to test the existence of evolutionary tradeoffs, characterize their general quality, and reveal their genetic origins. To examine the underlying mechanism for a fitness trade-off, we constructed the evolutionary trajectories of Escherichia coli K-12 at increasing temperatures up to 45.3°C, and found diverging mutational histories that led to adaptive phenotypes with and without fitness trade-offs at low temperatures. We identified genetic changes in cellular respiration, iron metabolism and methionine biosynthesis that regulated gene expression to achieve thermal adaptation and determined the presence and absence of a fitness trade-off. Our results suggested that evolutionary trade-off could be generated by a regulatory protein mutation that was beneficial in the selective conditions but forced suboptimal proteome allocation under non-selective environments.
2020-11-17 | GSE140478 | GEO
Project description:Protein synthesis is costly and the proteome size is constrained. Using a genome-scale computational model of proteome allocation together with absolute proteomics data sets from many growth environments, we determine how these fundamental limitations constrain growth and fitness in Escherichia coli. First, we show that the observed variation in growth rates across environments is largely determined by the expression of protein not utilized for growth in a given environment. We then elucidate the overall transcriptional regulatory logic that underlies the expression of unused protein. We systematically classify the unused proteome into segments devoted to environmental readiness and stress resistance functions. While expression of these proteome segments incurs a fitness cost of decreased growth in a fixed environment, they provide fitness benefits in a changing environment. Thus, the systems biology of the prokaryotic proteome can be quantitatively understood based on resource allocation to growth, environmental readiness, and stress resistance functions.
2018-08-01 | GSE72020 | GEO
Project description:Pleiotropic regulatory mutations affect diverse cellular processes, posing an explicit challenge to our multi-scale understanding of the genotype-phenotype relationships across multiple biological scales. Adaptive Laboratory Evolution (ALE) allows for such mutations to be found and characterized in the context of clear selection pressures. Here, several ALE-selected single-mutation variants in Escherichia coli’s RNA polymerase (RNAP) are detailed using an integrated multi-scale experimental and computational approach. While these mutations increase cellular growth rates in steady environments, they reduce tolerance to stress and environmental fluctuations. We detail structural changes in the RNAP that rewire the transcriptional machinery to rebalance proteome and energy allocation towards growth and away from several hedging and stress functions. SurprisinglyW, we find that while these mutations occur in diverse locations in the RNAP, they share a common adaptive mechanism. In turn, these findings highlight the resource allocation trade-offs organisms face and suggest how the structure of the regulatory network enhances evolvability.
2016-04-28 | GSE59377 | GEO
Project description:The transcriptome and DGE analysis of the fat body and ovary of L. migratoria based on the Illumina short-read sequencing technology and De novo assembly. Research on the trade-offs between immunity and reproduction is contributing significantly to the understanding of the fitness of organisms in nature.
2017-05-01 | GSE57437 | GEO
Project description:Fitness trade-offs lead to suppressor tolerance in yeast
| PRJEB14235 | ENA
Project description:Exploring molecular details of carbon utilization trade-offs in galactose-evolved yeast Adaptively evolved yeast mutants on galactose for around 400 generations showed diminished growth and carbon uptake rates on glucose. Genome-scale approaches were applied to characterize the molecular genetic basis of these trade-offs in carbon source utilization. Engineered mutants showing trade-offs in a specific carbon uptake rate between both carbons were used as controls. The transcriptional responses of the evolved mutants were almost identical during growth on both carbon sources. These carbon-independent conserved patterns were clearly observed in specific pathways and genes. Up-regulation of PGM2, a confirmed beneficial genetic change for improving galactose utilization was preserved on both carbons. In addition, HXK1, GLK1 and genes involved in reserve carbohydrate metabolism were up-regulated, while HXK2 was down-regulated. Genes that have a transcription factor binding site for Gis1p, Rph1p, Msn2/4p and Nrg1p were up-regulated. These results indicated changes in the metabolic pathways involved in metabolism of both carbons and in nutrient signaling pathway. The concentration profile of trehalose and glycogen supported these findings. Mutations in RAS2 and ERG5 genes were selected because of their beneficial and neutral effect on galactose utilization, respectively in our previous study. Site-directed mutants containing galactose-beneficial mutations in RAS2 only resulted in a significant decrease in glucose utilization. Integration of all these analyses clearly suggest an antagonistic pleiotropic trade-off in carbon source utilization caused by changes in regulatory region, and we hereby demonstrate how systems biology can be used to gain insight into evolutionary processes at the molecular level. Yeast galactose evolved mutants having improved galactose availability were grown on aerobic batch with glucose as carbon source
2012-07-31 | E-GEOD-39065 | biostudies-arrayexpress
Project description:The transcriptome and DGE analysis of the fat body and ovary of L. migratoria based on the Illumina short-read sequencing technology and De novo assembly. Research on the trade-offs between immunity and reproduction is contributing significantly to the understanding of the fitness of organisms in nature. The cDNA libraries for the mixed tissue samples of the fat body and ovary collected from the Sephadex group, the bacterial parasite group, and the dipteran parasite group at 4 hours and 6 days post-treatment were made for the DGE analysis. Every experimental treatment sample had one DGE-seq and one parallel replication.
2017-05-01 | E-GEOD-57437 | biostudies-arrayexpress
Project description:Tetranychus urticae is an important pest that causes severe damage on a wide variety of plants and crops, leading to a substantial loss of productivity. Previous research has focused on the study of Arabidopsis short-term response to T. urticae, but a comprehensive evaluation of the interaction through whole plant life cycle has not been previously studied. Here, through a physiological trait, transcriptomic and hormonomic evaluation we uncovered the molecular pathways directing the interaction of T. urticae during the complete plant life cycle. Upon mite infestation, plant suffers a process of adaptation to cope the stress and survive, led by the establishment of defence-growth trade-offs in the plant. Transcriptional and hormonal evaluation reveal how plant defence response upon mite perception determines the later growth responses and plant survival. In addition, a delay in plant development with a negative effect on plant fitness was observed, being fitness negatively affected with seed ageing. Taken together, our findings uncover the dynamics regulating plant-mite interactions and determining plant survival and reproductive success, providing new potential targets for improving plant response. Additionally, trade-offs suppose a cost on final plant fitness, demonstrating the underlying impact of the mite on the establishment of the offspring.
2024-08-31 | GSE255811 | GEO
Project description:Bacteria regulate their cellular resource allocation to enable their fast growth-adaptation to a variety of environmental niches. We studied the ribosomal allocation, growth and expression profile of two sets of fast-growing mutants of Escherichia coli K-12 MG1655. Mutants with 3 copies of the stronger ribosomal RNA operons grew faster than the wild-type strain in minimal media and show similar phenotype to previously studied rpoB mutants. All of them displayed increased ribosomal content, a longer diauxic shift and a reduced activity of the aceBAK operon, indicative of repressed gluconeogenic pathways. Transcriptomic profiles of fast-growing mutants showed common downregulation of hedging functions and upregulated growth functions. Proteome allocation estimations showed an increase in the growth-related proteome for fast-growing strains, but not an increased cellular budget for recombinant protein production. These results show that two different regulatory perturbations (rRNA promoters or rpoB mutations) increasing ribosomal allocation optimize the proteome for growth with a concomitant fitness cost.
2022-02-21 | GSE180830 | GEO
Project description:Exploring molecular details of carbon utilization trade-offs in galactose-evolved yeast Adaptively evolved yeast mutants on galactose for around 400 generations showed diminished growth and carbon uptake rates on glucose. Genome-scale approaches were applied to characterize the molecular genetic basis of these trade-offs in carbon source utilization. Engineered mutants showing trade-offs in a specific carbon uptake rate between both carbons were used as controls. The transcriptional responses of the evolved mutants were almost identical during growth on both carbon sources. These carbon-independent conserved patterns were clearly observed in specific pathways and genes. Up-regulation of PGM2, a confirmed beneficial genetic change for improving galactose utilization was preserved on both carbons. In addition, HXK1, GLK1 and genes involved in reserve carbohydrate metabolism were up-regulated, while HXK2 was down-regulated. Genes that have a transcription factor binding site for Gis1p, Rph1p, Msn2/4p and Nrg1p were up-regulated. These results indicated changes in the metabolic pathways involved in metabolism of both carbons and in nutrient signaling pathway. The concentration profile of trehalose and glycogen supported these findings. Mutations in RAS2 and ERG5 genes were selected because of their beneficial and neutral effect on galactose utilization, respectively in our previous study. Site-directed mutants containing galactose-beneficial mutations in RAS2 only resulted in a significant decrease in glucose utilization. Integration of all these analyses clearly suggest an antagonistic pleiotropic trade-off in carbon source utilization caused by changes in regulatory region, and we hereby demonstrate how systems biology can be used to gain insight into evolutionary processes at the molecular level.
2012-08-01 | GSE39065 | GEO