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.

Figure 1

Whole genome comparison of E. coli B REL606 and E. coli K-12 MG1655. Strain-specific regions are indicated by discontinuities on the diagonal line (those >10 kb are marked by arrows). Short vertical lines on each axis represent coding sequences that reside on the forward or reverse strand. Segments that occupy the same location on each genome and encode equivalent functions but are highly dissimilar are shown in bold. Except for those marked with asterisks, all the strain-specific regions coincide with genomic islands that were identified by genomic anomalies. Ticks are marked every 500 kb.

Figure 2

Transcription ratios of E. coli B REL606 to K-12 MG1655 at exponential (E) and stationary (S) growth phases during growth in LB medium. Internal lines were positioned at ±1.0 on both axes denoting log₂-transformed expression ratios. The numbers of genes within each range of expression ratios are shown. A functional category using the COG database [45] was assigned to each gene and color-coding was employed as follows: red circles, amino acid transport and metabolism; blue circles, cell motility; green circles, energy production and conversion; black circles, biogenesis of cell wall components; empty circles, other or unknown function.

Figure 3

Extracellular protein concentrations of E. coli B and E. coli K-12. Extracellular proteins were precipitated from the supernatants of each E. coli strain grown in LB and minimal R/2 media at the exponential (E) and stationary (S) growth phases.

Figure 4

Comparison of the transcriptomes, proteomes, and phenomes of E. coli B REL606 and E. coli K-12 MG1655 cultured in LB medium. In the individual thumbnail graphs, the x-axes denote exponential and stationary growth phases, and the y-axes show the transcription ratio (on a log₂ scale) of each gene in the B strain to that of the homologous gene in the K-12 strain. The transcription bars are coded red for up-regulation in B and green for up-regulation in K-12. Genes showing differences in transcriptional (or translational) levels of ≥2- or ≤0.5-fold in the exponential and/or stationary phase(s) are shown. The backgrounds of the graphs are grey if both transcriptional and translational differences were detected. Gene names are shown in red if the translational level was higher in the B strain and green if it was higher in K-12. The top of the figure shows extracellular proteins with more than a two-fold difference between the strains in the stationary phase on growth in minimal medium. Significant differences in cell growth on particular carbon sources, demonstrated by phenotype microarray tests, are shown at the bottom. Growth curves are green for B, red for K-12, and yellow for the overlapping region. Abbreviations are given in Additional file 1.

Figure 5

Proposed explanations for the observed and predicted phenotypes of E. coli B strains derived from the combined analysis of genome, transcriptome, and proteome data. In the inner circle, observations from this study are marked with a green background and hypotheses generated in this study are shown in pink. Genes with elevated mRNA or protein expression in B (red circle) or K-12 (green circle) strains are shown. Genetic differences between B and K-12 strains are denoted as follows: Δ, absence in B; -, pseudogene in B. Red arrows denote the phenotypes and related genetic backgrounds supported by flux balance analysis using the reconstructed metabolic model of the B strain.