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

Sung H. Yoon, Mee Jung Han, Haeyoung Jeong, Choong H. Lee, Xiao Xia Xia, Dae Hee Lee, Ji H. Shim, Sang Y. Lee, Tae K. Oh, Jihyun F. Kim

Research output: Contribution to journalArticle

81 Citations (Scopus)

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.

Original languageEnglish
Article numberR37
JournalGenome biology
Volume13
Issue number5
DOIs
Publication statusPublished - 2012 May 25

Fingerprint

Escherichia coli B
systems analysis
Systems Analysis
genome
Escherichia coli
phenotype
secretion
Genome
Phenotype
protein
heat shock
Escherichia coli K12
protein secretion
physiology
organisms
proteome
flagellum
genotype
recombinant proteins
Flagella

All Science Journal Classification (ASJC) codes

  • Ecology, Evolution, Behavior and Systematics
  • Genetics
  • Cell Biology

Cite this

Yoon, Sung H. ; Han, Mee Jung ; Jeong, Haeyoung ; Lee, Choong H. ; Xia, Xiao Xia ; Lee, Dae Hee ; Shim, Ji H. ; Lee, Sang Y. ; Oh, Tae K. ; Kim, Jihyun F. / Comparative multi-omics systems analysis of Escherichia coli strains B and K-12. In: Genome biology. 2012 ; Vol. 13, No. 5.
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Yoon, SH, Han, MJ, Jeong, H, Lee, CH, Xia, XX, Lee, DH, Shim, JH, Lee, SY, Oh, TK & Kim, JF 2012, 'Comparative multi-omics systems analysis of Escherichia coli strains B and K-12', Genome biology, vol. 13, no. 5, R37. https://doi.org/10.1186/gb-2012-13-5-r37

Comparative multi-omics systems analysis of Escherichia coli strains B and K-12. / Yoon, Sung H.; Han, Mee Jung; Jeong, Haeyoung; Lee, Choong H.; Xia, Xiao Xia; Lee, Dae Hee; Shim, Ji H.; Lee, Sang Y.; Oh, Tae K.; Kim, Jihyun F.

In: Genome biology, Vol. 13, No. 5, R37, 25.05.2012.

Research output: Contribution to journalArticle

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AU - Yoon, Sung H.

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AU - Jeong, Haeyoung

AU - Lee, Choong H.

AU - Xia, Xiao Xia

AU - Lee, Dae Hee

AU - Shim, Ji H.

AU - Lee, Sang Y.

AU - Oh, Tae K.

AU - Kim, Jihyun F.

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Y1 - 2012/5/25

N2 - 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.

AB - 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.

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