The evolution of low mutation rates in experimental mutator populations of Saccharomyces cerevisiae
ABSTRACT: microarray experiment to test the gene expression in long term lines of mutator and non-mutator yeast. Here we use an experimental evolution approach to investigate the conditions required for evolution of a reduction in mutation rate and the mechanisms by which populations tolerate the accumulation of deleterious mutations. We find that after ~6700 generations four out of eight experimental mutator lines had evolved a decreased mutation rate. 2 condition experiment, derived experimental evolution strains compared to their ancestor strain. We compared the expression profile of one of the mutator lines (m8) after 6700 generations with its mutator ancestor, and as a control, an evolved non mutator after 6700 generations was compared to to its non-mutator ancestor. In order to prepare cells for expression microarray, glass tubes containing 3 ml of YPD were inoculated from overnight cultures, and grown until the OD600 was approximately 0.3.
Project description:During a 1,000 generations evolution experiment, two types of bacteria (S and L) repeatedly diverged from a common ancestor (A) in a fully sympatric seasonal environment containing glucose and acetate. We compare the transcription profile of the two derived types and the common ancestor in order to investigate the metabolic modifications associated with this adaptive diversification event. Keywords: time point, experimental evolution Overall design: Total RNA was extracted at 4 different time points of the 24H kinetic growth curve of each of the 3 types of bacteria (S, L and A). At each time point, S and L transcription profiles were compared to A. Each comparison was performed in 5 biological replicates.
Project description:Microbial populations founded by a single clone and propagated under resource limitation can become polymorphic. We sought to understand how stable polymorphism arose in an Escherichia coli population that evolved for 765 generations under continuous glucose limitation. Apart from a 29 kb deletion in the dominant clone, no large-scale genomic changes distinguish evolved clones from their common ancestor. However, when co-evolved clones are cultured separately their transcriptional profiles differ markedly from that ancestor, and do so in ways that are consistent with our understanding of how E. coli adapts to glucose limitation. All adaptive clones exhibit reduced activity of the stationary-phase sigma factor σS and increased expression of glucose transport genes, including the glycoporin LamB and the galactose transporter MglABC. Other expression differences, such as up-regulation of acetyl-CoA synthetase, are clone-specific and confirm previous reports of acetate cross-feeding in this system. When co-evolved clones are cultured together, transcription profiling reveals another class of genes whose expression in the dominant clone differs from that observed when the clone is cultured by itself. Many of these genes are part of the CpxR-mediated stress response. CpxR activation in monoculture likely results from extracellular accumulation of acetate that is removed by acetate-scavenging strains in co-culture. Targeted gene sequencing reveals that global regulatory mutations in σS as well as small-scale regulatory mutations in the maltose and acetyl CoA synthetase operons contribute to the evolution of cross-feeding. Finally, we identified two mutations in the founder that likely pre-disposed the experimental population to develop specialists that thrive on overflow metabolites. Subsequent mutations that lead to specialization emphasize the importance of compensatory rather than gain-of-function mutations in this system. Observations that polymorphism readily evolves in an asexual population, that adaptive mutants arise without large-scale change in genome architecture, and that morphs have both common and unique patterns of gene expression influenced by whether they are cultured separately or together, underscore the importance of regulatory change, founder genotype, and the biotic environment in the adaptive evolution of microbes. Four isolates of E. coli evolved under long-term glucose limitation and their common ancestor were grown in Luria broth to stationary phase. Genomic DNA from each of the evolved isolates was competitively hybridized against genomic DNA from the ancestral strain.
Project description:Genome-wide assays to test the interaction between two independently evolved mechanisms of fluconazole resistance Keywords: Comparative genomic hybridization Overall design: Three populations at 100 and 400 generations of evolution in increasing concentrations of fluconazole [experiment 1 - (Anderson et al.,2003 Genetics,163:1287-98, PMID: 12702675, http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=pubmed&term=12702675)], a single double-mutant (progeny strain from each of the three crosses of the strains from generation 100, and the erg3r mutant strain, were all assayed for gene expression against sce13 the ancestor strain.
Project description:We conducted a set of lab-evolution experiments in yeast and followed the long-term dynamics of aneuploidy under diverse conditions including heat shock and high PH. Each evolution experiment starts with an ancestor strain that was subjected (in several independent repetitions) to certain growth conditions such as high temperature 39°C, permissive temperature 30°C, gradually increasing temperature from 30°C to 39°C, high pH=8.6 and normal PH. In all cases the mRNA extraction was performed on a population sample that was grown for 18 generations under stress-less conditions. This is since we aimed to measure the gene expression changes that are due to stress adaptation and not the physiological response.
Project description:Investigation of gene expression changes in a DvH genotype ES10-5, a strain isolated from population ES10 which has been evolved under salt stress for 5000 generations. The gene expression was compared to a gentype ES9-11 isolated from ES9 evolved under the same condition for 1200 generations and the ancestral strain. The genotype ES10-5 was characterized in this study. ES9-11 was isolated and characterized in Zhou A et al., 2013. Characterization of NaCl tolerance in Desulfovibrio vulgaris Hildenborough through experimental evolution. ISME J, 7(9), 1790-1802 Overall design: Basal gene expression changes in salt-stressed evolved genotype 5000g-ES10-5 was examined and compared with salt-stress evolved genotype 1200g-ES9-11 and ancestor at mid-logarithmic phase in standard growth medium LS4D. The transcriptional responses to high salinity in evolved genotypes ES10-5 and ES9-11 and ancestor were characterized by comparing the gene expressions at mid-logarithmic phase under high salinity (LS4D+300 mM NaCl) to standard growth condition LS4D. Total RNA isolated from three replicates of salt-stress evolved 5000g-ES10-5,1200g-ES9-11, or ancestral DvH was labeled with Cy3 and co-hybridized with Cy5-labeled DvH gDNA to the individual array on a custom 12-plex NimbleGen oligonucleotide array.
Project description:Using data from microarray experiments, we investigated the transcriptional changes in evolved and ancestor D. vulgaris strains. gene expression changes in evolved salt-stressed DvH strain (ES, evolved in LS4D + 100 mM NaCl for 1200 generations), evolved control DvH strain (EC, evolved in LS4D for 1200 generations) and ancestor DvH strain grown in non-stress (LS4D), low salt stress (LS4D + 100 mM NaCl) or high salt stress (LS4D + 250 mM NaCl) conditions Comparison of gene expression in evolved salt-stressed strain (ES, 1200g) to ancestor (An) or evolved control (EC, 1200g) strains at mid-logarithmic phase under standard growth condition with defined medium LS4D, salt stress conditions LS4D+100 mM NaCl or LS4D+250 mM NaCl.
Project description:An Eschericia coli strain was constructed in which the PaeR7 restriction-modification gene complex was present under an unstable condition on a partially duplicated chromosomal region so that it may continuously attack the host genome to accelerate its evolution. This strain was grown for more than a hundred of generations through repeated cycles of saturation and dilution. The winners of this competition showed faster growth than the ancestor. Analysis of their genome and transcriptome revealed that they have acquired rearrangements in genes affecting their growth. The global expression pattern changes may have realized growth advantage during the adaptation experiment. Keywords: time course during adaptive evloution Overall design: We used microarrays to know the genetic mechanism underlying adaptive evolution process, and to know the global expression changes that realize advantage in growth during adaptation. Four populations of the parent strain (YA027) and two populations of isogenic r-m+ strain (YA074), for control, were grown and serially propagated in amino acid rich medium (Davis’s MM supplied with 20 amino acids) with Cm (chloramphenicol) and Km (kanamycin), daily with 100-fold dilution. One passage corresponds to 6 - 7 generations, though it might be changed with evolution. Their growth was monitored daily. The growth curve shifted upwards every day in every population, reflecting improvement both in the initial growth rate and the saturation cell density through the evolution. To follow genome changes and global expression changes during adaptive evolution, we selected clones that might represent several stages of evolution with respect to growth from an r+m+ population (population #3) at the 11th, 84th, and 172th passage (corresponding 70, 500, and 1000 generations, respectively): 3-11-2, 3-11-4, 3-11-9, and 3-11-10 from the 11th passage; 3-84-2, 3-84-4, 3-84-6, and 3-84-10 from the 84th passage, and 3-172-1, 3-172-9, and 3-172-10 from the 172nd passage. We subjected them to transcriptome analysis. All gene expression measurements were duplicated or triplicated.
Project description:Gene duplication and deletion are pivotal processes shaping the structural and functional repertoire of genomes, with implications for disease, adaptation and evolution. We employed an experimental evolution framework partnered with high-throughput genomics to assess the molecular and transcriptional characteristics of novel gene copy-number variants (CNVs) in Caenorhabditis elegans populations subjected to varying intensity of selection. Here, we report a direct spontaneous genome-wide rate of gene duplication of 2.9 × 10-5 /gene/generation in C. elegans, the highest for any species to date. The increase in average transcript abundance of new duplicates arising under minimal selection is significantly greater than two-fold compared to single-copies of the same gene, suggesting that genes in segmental duplications are frequently overactive at inception. The average increase in transcriptional activity of gene duplicates is greater in MA lines that passed through single individual bottlenecks than in MA lines with larger population bottlenecks. Furthermore, there is an inverse relationship between the ancestral transcription levels of newly originating gene duplicates and population size, with duplicate copies of highly expressed genes less likely to accumulate in larger populations. The results demonstrate that there is a fitness cost of superfluous gene expression and purifying selection against new gene duplicates. However, on average, duplications also provide a significant increase in gene expression that can facilitate adaptation to novel environmental challenges. Overall design: Experimental evolution study of 35 mutation accumulation lines descendant from a common ancestor: Twenty lines of size N = 1, ten lines of population size N = 10, and five lines of population size N = 100 are compared to their ancestor after up to 409 generations of mutation accumulation.
Project description:This study compared the genome of Streptomyces rimosus rimosus against that of Streptomyces coelicolor. It also compared 4 strains with changes in oxytetracycline production and derived from G7, the type strain, against G7. Duplicate samples, each replicate may be found in the corresponding supplementary file for the Sample
Project description:One of the central goals of evolutionary biology is to explain and predict the molecular basis of adaptive evolution. We studied the evolution of genetic networks in Saccharomyces cerevisiae (budding yeast) populations propagated for more than 200 generations in different nitrogen-limiting conditions. We find that rapid adaptive evolution in nitrogen-poor environments is dominated by the de novo generation and selection of copy number variants (CNVs), a large fraction of which contain genes encoding specific nitrogen transporters including PUT4, DUR3 and DAL4. The large fitness increases associated with these alleles limits the genetic heterogeneity of adapting populations even in environments with multiple nitrogen sources. Complete identification of acquired point mutations, in individual lineages and entire populations, identified heterogeneity at the level of genetic loci but common themes at the level of functional modules, including genes controlling phosphatidylinositol-3-phosphate metabolism and vacuole biogenesis. Adaptive strategies shared with other nutrient-limited environments point to selection of genetic variation in the TORC1 and Ras/PKA signaling pathways as a general mechanism underlying improved growth in nutrient-limited environments. Within a single population we observed the repeated independent selection of a multi-locus genotype, comprised of the functionally related genes GAT1, MEP2 and LST4. By studying the fitness of individual alleles, and their combination, as well as the evolutionary history of the evolving population, we find that the order in which these mutations are acquired is constrained by epistasis. The identification of repeatedly selected variation at functionally related loci that interact epistatically suggests that gene network polymorphisms (GNPs) may be a frequent outcome of adaptive evolution. Our results provide insight into the mechanistic basis by which cells adapt to nutrient-limited environments and suggest that knowledge of the selective environment and the regulatory mechanisms important for growth and survival in that environment greatly increases the predictability of adaptive evolution. DNA from each evolved clone or population is hybridized vs DNA from the ancestral strain