Scleractinian Coral
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ABSTRACT:
PROVIDER: PRJNA1116348 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:The evolutionary transition of multicellular life initially involves growth in groups of undifferentiated cells followed by differentiation into soma and germ-like cells. This is facilitated by trade-offs between traits determining survival and reproduction, favoring the coexistence of cells with extreme trait values and a convex trade-off curve as the multicellular state dominates. However, these transitions remain poorly characterized at the ecological and genetic level. Here, we studied the evolution of cell groups in ten isogenic lines of the unicellular green algae Chlamydomonas reinhardtii with prolonged exposure to a rotifer predator. We confirmed that this trait was heritable and characterized by a convex trade-off curve between reproduction and survival. Identical mutations evolved in all cell group isolates which were linked to survival and reducing associated cell costs. Overall, we show that just 500 generations of predator selection is sufficient to lead to a convex trade-off and incorporate evolved changes into the prey genome.
2021-02-13 | GSE166685 | 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. 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:Trade-offs often occurs during experimental evolution. For example, the degeneration of growth in glucose was found in a galactose adapted yeast. Here, we isolated one Lactococcus lactis mutant using experimental on maltose. The mutant grows normally on glucose, but faster than the wild-type on maltose and galactose. DNA microarray analysis and whole genome re-sequencing were applied to disclose the crucial points that determine the phenotype.
2016-12-31 | GSE56042 | 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
Project description:Escherichia coli, the common inhabitant of the mammalian intestine, exhibits considerable intraspecies genomic variation, which has been suggested to reflect adaptation to different ecological niches. Also, regulatory trade-offs, e.g., between catabolic versatility and stress protection, are thought to result in significant physiological differences between strains. For these reasons, the relevance of experimental observations made for âdomesticatedâ E. coli strains with regard to the behaviour of this species in its natural environments is often questioned and frequently doubts are raised on the status of E. coli as a defined species. We therefore investigated the variability of important eco-physiological functions such as carbon substrate uptake and breakdown capabilities as well as stress defence mechanisms in the genomes of commensal and pathogenic E. coli strains. Furthermore, eco-physiological properties of environmental strains were compared to standard laboratory strain K-12 MG1655. Catabolic, stress protection, and carbon- and energy source transport operons showed a very low intraspecies variability in 57 commensal and pathogenic E. coli. Environmental isolates adapted to glucose-limited growth in a similar way as E. coli MG1655, namely by increasing their catabolic flexibility and by inducing high affinity substrate uptake systems. Our results indicate that the major eco-physiological properties are highly conserved in the natural population of E. coli. This questions the proposed dominant role of horizontal gene transfer for niche adaptation. Keywords: comparative genomic hybridisation Standard approach for comparative genomic hybrisisation, 5 environmental strains were analysed on commercial E. coli MG1655 arrays (MWG), for each strains, biological replicates were done (separate LB cultures)
2006-12-04 | E-GEOD-6407 | biostudies-arrayexpress
Project description:Central carbon metabolism is highly conserved across microbial species, but can catalyze very different pathways depending on the organism and their ecological niche. Here, we study the dynamic reorganization of central metabolism after switches between the two major opposing pathway configurations of central carbon metabolism, glycolysis, and gluconeogenesis in Escherichia coli, Pseudomonas aeruginosa, and Pseudomonas putida. We combined growth dynamics and dynamic changes in intracellular metabolite levels with a coarse-grained model that integrates fluxes, regulation, protein synthesis, and growth and uncovered fundamental limitations of the regulatory network: After nutrient shifts, metabolite concentrations collapse to their equilibrium, rendering the cell unable to sense which direction the flux is supposed to flow through the metabolic network. The cell can partially alleviate this by picking a preferred direction of regulation at the expense of increasing lag times in the opposite direction. Moreover, decreasing both lag times simultaneously comes at the cost of reduced growth rate or higher futile cycling between metabolic enzymes. These three trade-offs can explain why microorganisms specialize for either glycolytic or gluconeogenic substrates and can help elucidate the complex growth patterns exhibited by different microbial species.
2022-01-11 | MTBLS3887 | MetaboLights
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:Escherichia coli, the common inhabitant of the mammalian intestine, exhibits considerable intraspecies genomic variation, which has been suggested to reflect adaptation to different ecological niches. Also, regulatory trade-offs, e.g., between catabolic versatility and stress protection, are thought to result in significant physiological differences between strains. For these reasons, the relevance of experimental observations made for “domesticated” E. coli strains with regard to the behaviour of this species in its natural environments is often questioned and frequently doubts are raised on the status of E. coli as a defined species. We therefore investigated the variability of important eco-physiological functions such as carbon substrate uptake and breakdown capabilities as well as stress defence mechanisms in the genomes of commensal and pathogenic E. coli strains. Furthermore, eco-physiological properties of environmental strains were compared to standard laboratory strain K-12 MG1655. Catabolic, stress protection, and carbon- and energy source transport operons showed a very low intraspecies variability in 57 commensal and pathogenic E. coli. Environmental isolates adapted to glucose-limited growth in a similar way as E. coli MG1655, namely by increasing their catabolic flexibility and by inducing high affinity substrate uptake systems. Our results indicate that the major eco-physiological properties are highly conserved in the natural population of E. coli. This questions the proposed dominant role of horizontal gene transfer for niche adaptation. Keywords: comparative genomic hybridisation
2006-12-05 | GSE6407 | GEO