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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

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

Published: 25 May 2012

Additional files

Additional file 1:

Supplementary Methods, Figures S1 to S4, Tables S1 to S5, and Supplementary References. Supplementary Methods: preparation of whole cellular, membrane and extracellular proteins, two-dimensional gel electrophoresis and image analysis, and metabolite abbreviations in Figure 4. Figure S1: growth curves of E. coli B strains (REL606 and BL21(DE3) and K-12 strains (MG1655 and W3110) in complex LB medium and minimal R/2 medium supplemented with 10 g/l glucose. Figure S2: total cellular, outer membrane, and extracellular proteomes of the E. coli strains. Figure S3: phenotype microarray comparison of E. coli B REL606 and K-12 MG1655. Figure S4: phylogenetic position of two T2S systems in E. coli B REL606. Table S1: pseudogene comparison between E. coli B REL606 and K-12 MG1655. Table S2: genes that were highly expressed at both the exponential and stationary growth phases during growth of E. coli B REL606 and K-12 MG1655 in LB medium. Table S3: proteins exhibiting significant quantitative differences between E. coli B and K-12 strains. Table S4: metabolic reactions modified in the metabolic network model for E. coli B REL606 compared to the model for E. coli K-12 MG1655. Table S5: phenotypic differences of E. coli B REL606 and K-12 MG1655 in PM1 and PM2 and in silico predictions of cell growth on each carbon source. Supplementary References.

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