Abstract
Physical and functional interactions define the molecular organization of the cell. Genetic interactions, or epistasis, tend to occur between gene products involved in parallel pathways or interlinked biological processes. High-throughput experimental systems to examine genetic interactions on a genome-wide scale have been devised for Saccharomyces cerevisiae, Schizosaccharomyces pombe, Caenorhabditis elegans and Drosophila melanogaster, but have not been reported previously for prokaryotes. Here we describe the development of a quantitative screening procedure for monitoring bacterial genetic interactions based on conjugation of Escherichia coli deletion or hypomorphic strains to create double mutants on a genome-wide scale. The patterns of synthetic sickness and synthetic lethality (aggravating genetic interactions) we observed for certain double mutant combinations provided information about functional relationships and redundancy between pathways and enabled us to group bacterial gene products into functional modules.
NOTE: In the version of this article initially published online two author names (Gabriel Moreno-Hagelseib and Constantine Christopolous) were spelled incorrectly. The correct author names are Gabriel Moreno-Hagelsieb and Constantine Christopoulos. The error has been corrected for the print, PDF and HTML versions of this article.
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Change history
17 August 2008
NOTE: In the version of this article initially published online two author names (Gabriel Moreno-Hagelseib and Constantine Christopolous) were spelled incorrectly. The correct author names are Gabriel Moreno-Hagelsieb and Constantine Christopoulos. The error has been corrected for the print, PDF and HTML versions of this article.
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Acknowledgements
We thank M. Costanzo for comments on the manuscript. This work was supported by a Canadian Institute of Health Research (CIHR) grant (82852) to J.F.G. and A.E., by a US National Institutes of Health grant to B.L.W. (GM62662), by Grant-in-Aid for Scientific Research on Priority Areas from the Ministry of Education, Sports, Science and Technology of Japan Core Research for Evolutional Science and Technology, and Japan Science and Technology grants to H.M., by a CIHR grant (GSP-41567) to B.J.A. and C.B., by a partial postdoctoral fellowship from the Mexican Science and Technology Research Council to J.J.D.-M., and by a Laboratory Directed Research and Development grant to G.B. The phage-λ Red system was kindly provided by D.L. Court (National Cancer Institute).
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Authors and Affiliations
Contributions
M.B. and G.B. coordinated experimental design and data analysis. M.B., G.B., H.L., J.W., P.V., C.C., L.L., M.A., K.A.D., N.Y., H.M. and B.L.W. performed optimization studies and constructed recipient arrays. J.L., A.S.-N., W.Y., A.G.G., O.P., G.B. and M.B. generated query deletion knockouts. M.B., F.B., N.S., S.C., J.-Y.C. and A.N.-A. performed genome-wide screens. M.B., S.P., A.D., S.J., B.S., H.D., B.J.A. and C.B. designed and performed quantitative image analysis. J.J.D.-M., M.B., S.P. and G.M.-H. performed informatics analyses. G.B., B.G. and W.Y. performed validation experiments. G.B., M.B., J.F.G. and A.E. drafted the manuscript. J.F.G. and A.E. conceived, designed and directed the project.
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Supplementary Text and Figures
Supplementary Figures 1–5, Supplementary Methods, Supplementary Results, Supplementary Discussion (PDF 1941 kb)
Supplementary Table 1
List of recipient F- KEIO deletion mutant strains and SPA-tagged essential genes used in this study. (XLS 701 kb)
Supplementary Table 2
List of query deletion mutant strains used in the 39 genome-wide screens. (XLS 32 kb)
Supplementary Table 3
High-confidence genetic interaction filtered after accounting for linkage (30 kbp-window) using a stringent cut-off of |Z score| > = 4 (P < 0.0001). (XLS 284 kb)
Supplementary Table 4
Raw colony sizes (see Sheet 1), Normalized median colony sizes (see Sheet 2), |Z scores| (see Sheet 3) and interaction (S) scores (see Sheet 4) of each mutant gene pair from 39 genome-wide screens without any filtering parameters. (XLS 35759 kb)
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Butland, G., Babu, M., Díaz-Mejía, J. et al. eSGA: E. coli synthetic genetic array analysis. Nat Methods 5, 789–795 (2008). https://doi.org/10.1038/nmeth.1239
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DOI: https://doi.org/10.1038/nmeth.1239