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E-GEOD-17276 - Transcriptional profiling of an evolved polymorphism in E. coli

Released on 16 May 2010, last updated on 1 May 2014
Escherichia coli K-12
Samples (82)
Array (1)
Protocols (6)
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 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.
Experiment type
transcription profiling by array 
Frank Rosenzweig <>, Margie A Kinnersley, William E Holben
Investigation descriptionE-GEOD-17276.idf.txt
Sample and data relationshipE-GEOD-17276.sdrf.txt
Raw data (1)
Processed data (1)
Array designA-GEOD-8872.adf.txt
R ExpressionSetE-GEOD-17276.eSet.r