Perceiving molecular evolution processes in Escherichia coli by comprehensive metabolite and gene expression profiling.

Genome Biology
Chandran VijayendranErwin Flaschel

Abstract

Evolutionary changes that are due to different environmental conditions can be examined based on the various molecular aspects that constitute a cell, namely transcript, protein, or metabolite abundance. We analyzed changes in transcript and metabolite abundance in evolved and ancestor strains in three different evolutionary conditions - excess nutrient adaptation, prolonged stationary phase adaptation, and adaptation because of environmental shift - in two different strains of bacterium Escherichia coli K-12 (MG1655 and DH10B). Metabolite profiling of 84 identified metabolites revealed that most of the metabolites involved in the tricarboxylic acid cycle and nucleotide metabolism were altered in both of the excess nutrient evolved lines. Gene expression profiling using whole genome microarray with 4,288 open reading frames revealed over-representation of the transport functional category in all evolved lines. Excess nutrient adapted lines were found to exhibit greater degrees of positive correlation, indicating parallelism between ancestor and evolved lines, when compared with prolonged stationary phase adapted lines. Gene-metabolite correlation network analysis revealed over-representation of membrane-associated functional ca...Continue Reading

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Methods Mentioned

BETA
PCA
electrophoresis

Software Mentioned

MGStat
Cytoscape
Xcalibur
SAM
ImaGene
Adp
Excel
GeneSight
MASCOT
Matlab

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