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


ABSTRACT: BACKGROUND: 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 testing. This systems analysis revealed that E. coli B is 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 has 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 strains 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 conditions but also to design recombinant hosts.

SUBMITTER: Yoon SH 

PROVIDER: S-EPMC3446290 | biostudies-literature | 2012

REPOSITORIES: biostudies-literature

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

Yoon Sung Ho SH   Han Mee-Jung MJ   Jeong Haeyoung H   Lee Choong Hoon CH   Xia Xiao-Xia XX   Lee Dae-Hee DH   Shim Ji Hoon JH   Lee Sang Yup SY   Oh Tae Kwang TK   Kim Jihyun F JF  

Genome biology 20120525 5


<h4>Background</h4>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.<h4>Results</h4>We present a comprehensive analysis of genome-wide measurements incorporating multifaceted holistic data - genome, transcriptome  ...[more]

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