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Invited talk (6): 4:15 p.m. - 4:50 p.m.

Genetic Interaction Network in E. coli


Hirotada Mori, Professor, Graduate School of Biological Sciences, Nara Institute of Science and Technology, Japan


Escherichia coli, is undoubtedly one of the best-studied organisms and many of analysis tools are available. In addition to those, the comprehensive experimental resources, such as ORF clones, promoter fragment and single gene deletion libraries, have been established. This is clearly a big advantage to analyze this bacterium in the field of high-throughput biology and systems biology to build up models both in qualitatively and quantitatively both in science and industrial purposes.

We have long been performing constructions of comprehensive resources as one of the tools for large scale post-genomic analyses for last 10 years and we have established three ORF clone and two single gene deletion libraries. Two types sRNA gene deletion libraries have also been almost constructed.

"Robustness" of cell system, which is one of the major causes to make breeding difficult, is also one of the important subjects to be elucidated in the Systems Biology. To access this problem, understanding of global network system is needed because inactivation of a certain gene may be compensated by immediate reconstruction of cellular genes network. To elucidate this problem, we are now challenging Ågsynthetic lethal/sicknessÅh analysis by combinatorial double genes knockout. Our method is combination of two single gene knockout by recombination.

To perform this, we have constructed two types of single deletion libraries carrying different antibiotic resistance and developed the tool to control host cell sexuality. F plasmid determines the E. coli mating type and its integration into the host chromosome is called Hfr (High Frequency of Recombination). Once switching a deletion strain to donor by F derived tool, then combinatorial conjugation with entire set of single gene knockout strains can be performed. Quantification was done by scanning of colony growth at every 30min.

I will introduce our current progress towards comprehensive genetic interaction analysis.

More information,

  1. Butland G, Babu M, Diaz-Mejia JJ, Bohdana F, Phanse S, Gold B, Yang W, Li J, Gagarinova AG, Pogoutse O, Mori H, Wanner BL, Lo H, Wasniewski J, Christopolous C, Ali M, Venn P, Safavi-Naini A, Sourour N, Caron S, Choi JY, Laigle L, Nazarians-Armavil A, Deshpande A, Joe S, Datsenko KA, Yamamoto N, Andrews BJ, Boone C, Ding H, Sheikh B, Moreno-Hagelseib G, Greenblatt JF, & Emili A (2008) eSGA: E. coli synthetic genetic array analysis. Nat Methods 5:789-795.
  2. Typas A, Nichols RJ, Siegele DA, Shales M, Collins SR, Lim B, Braberg H, Yamamoto N, Takeuchi R, Wanner BL, Mori H, Weissman JS, Krogan NJ, & Gross CA (2008) High-throughput, quantitative analyses of genetic interactions in E. coli. Nat Methods 5:781-787.