Email updates

Keep up to date with the latest news and content from Genome Biology and BioMed Central.

Open Access Highly Accessed Research

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

Sung Ho Yoon1, Mee-Jung Han23, Haeyoung Jeong1, Choong Hoon Lee145, Xiao-Xia Xia2, Dae-Hee Lee1, Ji Hoon Shim1, Sang Yup Lee26, Tae Kwang Oh7 and Jihyun F Kim15*

Author affiliations

1 Systems and Synthetic Biology Research Center, Korea Research Institute of Bioscience and Biotechnology, Yuseong, Daejeon 305-806, Korea

2 Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering, BioProcess Engineering Research Center, Center for Systems and Synthetic Biotechnology, and Institute for the BioCentury, Korea Advanced Institute of Science and Technology, Yuseong, Daejeon 305-701, Korea

3 Department of Biomolecular and Chemical Engineering, Dongyang University, Yeongju, Gyeongbuk, 750-711, Korea

4 Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Yuseong, Daejeon 305-701, Korea

5 Department of Systems Biology, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 120-749, Korea

6 Department of Bio and Brain Engineering, and Bioinformatics Research Center, Korea Advanced Institute of Science and Technology, Yuseong, Daejeon 305-701, Korea

7 21C Frontier Microbial Genomics and Applications Center, Korea Research Institute of Bioscience and Biotechnology, Yuseong, Daejeon 305-806, Korea

For all author emails, please log on.

Citation and License

Genome Biology 2012, 13:R37  doi:10.1186/gb-2012-13-5-r37

Published: 25 May 2012

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.