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Series GSE17276 Query DataSets for GSE17276
Status Public on Jul 25, 2009
Title Transcriptional profiling of an evolved polymorphism in E. coli
Platform organism Escherichia coli str. K-12 substr. MG1655
Sample organism Escherichia coli K-12
Experiment type Expression profiling by array
Summary 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.
 
Overall design 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.
 
Contributor(s) Kinnersley MA, Rosenzweig F, Holben WE
Citation(s) 19893610
Submission date Jul 23, 2009
Last update date Mar 21, 2012
Contact name Frank Rosenzweig
E-mail(s) Frank.Rosenzweig@mso.umt.edu
Organization name University of Montana
Department Division of Biological Sciences
Street address 32 Campus Drive, HS 104
City Missoula
State/province MT
ZIP/Postal code 59812
Country USA
 
Platforms (1)
GPL8872 Rosenzweig_E.coli_4290_v1.0
Samples (41)
GSM432640 ancestor versus CV101 biological replicate 1, sample A, hybridization 1
GSM432641 ancestor versus CV101 biological replicate 1, sample A, hybridization 2
GSM432642 ancestor versus CV101 biological replicate 1, sample B, hybridization 1
This SubSeries is part of SuperSeries:
GSE17314 Evolved polymorphism in E. coli
Relations
BioProject PRJNA123669

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE17276_RAW.tar 60.6 Mb (http)(custom) TAR (of GPR)
Processed data included within Sample table
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