Evolved polymorphism in E. coli
Ontology highlight
ABSTRACT:
ORGANISM(S): Escherichia coli K-12
SUBMITTER: Frank Rosenzweig
PROVIDER: E-GEOD-17314 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
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 ÏS 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 ÏS 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 were grown in glucose-limited chemostat culture to steady state. Each isolate was grown separately (i.e in monoculture) in triplicate and three of the four (CV101, CV103, CV115 and CV116) were grown as a consortium in duplicate. Each experiment, or biological replicate, was sampled twice for monoculture experiments and once for consortium experiments. Total RNA from each sample was competitvely hybridized against total RNA from the common ancestor of the isolates grown at the same time in a separate chemostat using the same feed medium. For monoculture experiments, three hybridizations were done for each experiment: two hybridizations comparison for the first sample and a single hybridization for the second (with the exception of sample Jv116-1A which was only hybridized twice due to lack of sufficient RNA). For consortium experiments, two hybridizations were done for each biological replicate.
2010-05-16 | E-GEOD-17276 | biostudies-arrayexpress
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 Ï?S 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 Ï?S 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.
2010-05-15 | E-GEOD-17277 | biostudies-arrayexpress
Project description:The model prokaryote Escherichia coli can exist as a either a commensal or a pathogen in the gut of diverse mammalian hosts. These associations, coupled with its ease of cultivation and genetic variability, have made E. coli a popular indicator organism for tracking the origin of fecal water contamination. Source tracking accuracy is predicated on the assumption that E. coli isolates recovered from contaminated water present a genetic signature characteristic of the host from which they originated. In this study, we compared the accuracy with which E. coli isolated from humans, bear, cattle and deer could be identified by standard fingerprinting methods used for library-based microbial source tracking (repetitive element PCR and pulsed-field gel electrophoresis) in relation to microarray-based analysis of genome content. Our results show that patterns of gene presence or absence were more useful for distinguishing E. coli isolates from different sources than traditional fingerprinting methods, particularly in the case of human strains. Host-associated differences in genome composition included the presence or absence of mobile IS1 elements as well as genes encoding the ferric dicitrate iron transporter (fec), E. coli common pilus (ECP), type 1 fimbriae and the CRISPR associated cas proteins. Many of these differences occurred in regions of the E. coli chromosome previously shown to be M-bM-^@M-^\hot spotsM-bM-^@M-^] for the integration of horizontally-acquired DNA. PCR primers designed to amplify the IS1 and fec loci confirmed array results and demonstrated the ease with which gene presence/absence data can be converted into a diagnostic assay. The data presented here suggest that, despite the high level of genetic diversity observed among isolates by PFGE, human-derived strains may constitute a distinct ecotype distinguished by multiple potential library-independent source tracking markers. Twelve isolates of E. coli ( 3 from bear, 3 from cattle, 3 from deer and 3 from humans) were isolated from feces and/or raw sewage. Genome content for each strain was assessed in duplicate using comparative genome hybridization with E. coli K12 MG1655 as the reference for a total of 24 arrays.
2013-03-01 | E-GEOD-21115 | biostudies-arrayexpress
Project description:Microarray were done on 4 independent cultures. PA01 was grown for 6 hours to late log growth phase (OD600 0.9-1.0) in liquid BM2-swarming media under shaking conditions(swimming) or for 18 hours at 37C on BM2-swarming plate containing 0.5% (w/v) agar and 0.1% casamino acids. Cells were harvested either by centrifugation(swimming) or by a sterile inoculating loop (swarming) and were resuspended n BM2-swarming media supplement with RNAprotect reagent (Qiagen)
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2015-05-04 | E-GEOD-68492 | biostudies-arrayexpress
Project description:Five biological repeats of P.aeruginosa PA14 and five biological repeats of P.aeruginosa PA14 metR::phoA were grown in liquid BM2 swarming media containing 62mM potassium phosphate buffer [pH7], 2 mM MgSO4, 10uM FeSO4, 0.4% (wt/vol) glucose, and 0.1% (wt/vol) casamino acids. Microarray experiments were done using microarray slides and protocols from TIGR on samples taken from mid-log phase (OD600 0.4-0.5)cells.
2009-08-20 | E-FPMI-19 | biostudies-arrayexpress
Project description:We found that many of the genes for which mutants could not be obtained using promoterless aphA-3 gene replacement were annotated as acquired via horizontal gene transfer or as encoding hypothetical proteins. We were curious about the explanation of this finding. The expression of these genes was therefore examined by microarray analysis. The microarray data showed many had undetectable expression. This led us to suspect that many of the unrecoverable mutants might have resulted from insufficient expression of the promoterless aphA-3 gene. S. sanguinis cultures at late log growth phase at 37 oC under microaerobic condition were used for microarray analysis. RNA from each of three independent samples was isolated by RNeasy mini kit (Qiagen, Valencia, CA). Spotted microarray slides were obtained from the Pathogen Functional Genomics Resource Center at JCVI. Each gene had four repeats in one spotted microarray slides. The microarray was performed according to the manufacturerM-bM-^@M-^Ys protocol. Each sample was divided into two parts and labeled by Cy5 and Cy3 dyes respectively for microarray. The microarray data were analyzed by programs TIGR Spotfinder and Midas to obtain the ratio of one dye to another dye for gene relative expression. Additionally, the ratio of dye intensity to background in a microarray slide was obtained after Spotfinder analysis. Absolute expression of each gene was represented by the average ratio of dye intensity to background for each slide.
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Project description:Transcriptional profiling of the wild-type and its htrA mutant. Identification of genes that are affected by the htrA mutation in P. gingivalis Keywords: Genetic modification Two-condition experiment, W83 vs. htrA mutant late-log growth phase. Biological replicates: 4 control, 4 mutant, independently grown. One replicate per array.
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