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.

Author: Sung Ho YoonMee-Jung HanHaeyoung JeongChoong Hoon LeeXiao-Xia XiaDae-Hee LeeJi Hoon ShimSang Yup LeeTae Kwang OhJihyun F Kim
Credits/Source: Genome Biology 2012, 13:R37

Published on: 2012-05-25

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