High-throughput, quantitative analyses of genetic interactions in E. coli

Athanasios Typas, Robert J. Nichols, Deborah A. Siegele, Michael Shales, Sean Collins, Bentley Lim, Hannes Braberg, Natsuko Yamamoto, Rikiya Takeuchi, Barry L. Wanner, Hirotada Mori, Jonathan S. Weissman, Nevan J. Krogan, Carol A. Gross

Research output: Contribution to journalArticle

163 Citations (Scopus)

Abstract

Large-scale genetic interaction studies provide the basis for defining gene function and pathway architecture. Recent advances in the ability to generate double mutants en masse in Saccharomyces cerevisiae have dramatically accelerated the acquisition of genetic interaction information and the biological inferences that follow. Here we describe a method based on F factor-driven conjugation, which allows for high-throughput generation of double mutants in Escherichia coli. This method, termed genetic interaction analysis technology for E. coli (GIANT-coli), permits us to systematically generate and array double-mutant cells on solid media in high-density arrays. We show that colony size provides a robust and quantitative output of cellular fitness and that GIANT-coli can recapitulate known synthetic interactions and identify previously unidentified negative (synthetic sickness or lethality) and positive (suppressive or epistatic) relationships. Finally, we describe a complementary strategy for genome-wide suppressor-mutant identification. Together, these methods permit rapid, large-scale genetic interaction studies in E. coli.

Original languageEnglish (US)
Pages (from-to)781-787
Number of pages7
JournalNature Methods
Volume5
Issue number9
DOIs
StatePublished - Aug 4 2008
Externally publishedYes

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Escherichia coli
Throughput
Genes
Genetic Fitness
Technology
Yeast
Saccharomyces cerevisiae
Genome

ASJC Scopus subject areas

  • Biotechnology
  • Biochemistry
  • Molecular Biology
  • Cell Biology

Cite this

Typas, A., Nichols, R. J., Siegele, D. A., Shales, M., Collins, S., Lim, B., ... Gross, C. A. (2008). High-throughput, quantitative analyses of genetic interactions in E. coli. Nature Methods, 5(9), 781-787. https://doi.org/10.1038/nmeth.1240

High-throughput, quantitative analyses of genetic interactions in E. coli. / Typas, Athanasios; Nichols, Robert J.; Siegele, Deborah A.; Shales, Michael; Collins, Sean; Lim, Bentley; Braberg, Hannes; Yamamoto, Natsuko; Takeuchi, Rikiya; Wanner, Barry L.; Mori, Hirotada; Weissman, Jonathan S.; Krogan, Nevan J.; Gross, Carol A.

In: Nature Methods, Vol. 5, No. 9, 04.08.2008, p. 781-787.

Research output: Contribution to journalArticle

Typas, A, Nichols, RJ, Siegele, DA, Shales, M, Collins, S, 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', Nature Methods, vol. 5, no. 9, pp. 781-787. https://doi.org/10.1038/nmeth.1240
Typas, Athanasios ; Nichols, Robert J. ; Siegele, Deborah A. ; Shales, Michael ; Collins, Sean ; Lim, Bentley ; Braberg, Hannes ; Yamamoto, Natsuko ; Takeuchi, Rikiya ; Wanner, Barry L. ; Mori, Hirotada ; Weissman, Jonathan S. ; Krogan, Nevan J. ; Gross, Carol A. / High-throughput, quantitative analyses of genetic interactions in E. coli. In: Nature Methods. 2008 ; Vol. 5, No. 9. pp. 781-787.
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