Comparative multi-omics systems analysis of Escherichia coli strains B and K-12

Elucidation of a genotype-phenotype relationship is critical to understand an organism at the whole-system level. Here, we demonstrate that comparative analyses of multi-omics data combined with a computational modeling approach provide a framework for elucidating the phenotypic characteristics of organisms whose genomes are sequenced.

Results: We present a comprehensive analysis of genome-wide measurements incorporating multifaceted holistic data - genome, transcriptome, proteome, and phenome - to determine the differences between Escherichia coli B and K-12 strains.

A genome-scale metabolic network of E. coli B was reconstructed and used to identify genetic bases of the phenotypes unique to B compared with K-12 through in silico complementation test.

This systems analysis revealed that E. coli B was well-suited for production of recombinant proteins due to a greater capacity for amino acid biosynthesis, fewer proteases, and lack of flagella.

Furthermore, E. coli B had an additional type II secretion system and a different cell wall and outer membrane composition predicted to be more favorable for protein secretion.

In contrast, E. coli K-12 showed a higher expression of heat shock genes and was less susceptible to certain stress conditions.

Conclusions: This integrative systems approach provides a high-resolution system-wide view and insights into why two closely related groups of E.

coli B and K-12 manifest distinct phenotypes. Therefore, systematic understanding of cellular physiology and metabolism of the strains is essential not only to determine culture condition and, but also to design recombinant hosts.

Published on: 2012-05-25

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