title: High-throughput, quantitative analyses of genetic interactions in E. coli.
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.
authors.affiliation: Department of Microbiology and Immunology, University of California at San Francisco, 600 16th Street, San Francisco, California 94158, USA.
authors.forename: Athanasios
authors.initials: A
authors.lastname: Typas
authors.forename: Robert J
authors.initials: RJ
authors.lastname: Nichols
authors.forename: Deborah A
authors.initials: DA
authors.lastname: Siegele
authors.forename: Michael
authors.initials: M
authors.lastname: Shales
authors.forename: Sean R
authors.initials: SR
authors.lastname: Collins
authors.forename: Bentley
authors.initials: B
authors.lastname: Lim
authors.forename: Hannes
authors.initials: H
authors.lastname: Braberg
authors.forename: Natsuko
authors.initials: N
authors.lastname: Yamamoto
authors.forename: Rikiya
authors.initials: R
authors.lastname: Takeuchi
authors.forename: Barry L
authors.initials: BL
authors.lastname: Wanner
authors.forename: Hirotada
authors.initials: H
authors.lastname: Mori
authors.forename: Jonathan S
authors.initials: JS
authors.lastname: Weissman
authors.forename: Nevan J
authors.initials: NJ
authors.lastname: Krogan
authors.forename: Carol A
authors.initials: CA
authors.lastname: Gross
mesh_terms: D003227:Conjugation, Genetic; D004926:Escherichia coli / Q000235:genetics*; D016680:Genome, Bacterial; D009154:Mutation