eSGA: E. coli synthetic genetic array analysis

• Published in: Nature methods Vol. 5; no. 9; pp. 789 - 795
• Main Authors: Phanse, Sadhna, Bohdana, Fedyshyn, Li, Joyce, Mori, Hirotada, Greenblatt, Jack F, Wasniewski, Jas, Caron, Simone, Venn, Pascal, Laigle, Ludovic, Díaz-Mejía, J Javier, Sheikh, Bilal, Sourour, Natalie, Babu, Mohan, Emili, Andrew, Nazarians-Armavil, Anaies, Choi, Ja-Yeon, Ding, Huiming, Datsenko, Kirill A, Ali, Mehrab, Andrews, Brenda J, Butland, Gareth, Boone, Charles, Yang, Wenhong, Safavi-Naini, Anahita, Lo, Henry, Gold, Barbara, Christopoulos, Constantine, Gagarinova, Alla G, Moreno-Hagelsieb, Gabriel, Deshpande, Avnish, Yamamoto, Natsuko, Wanner, Barry L, Joe, Sarah, Pogoutse, Oxana
• Format: Journal Article
• Language: English
• Published: New York Nature Publishing Group US 01-09-2008; Nature Publishing Group
• Subjects: Bioinformatics; Biological Microscopy; Biological Techniques; Biomedical and Life Sciences; Biomedical Engineering/Biotechnology; Biotechnology; Brewer's yeast; Caenorhabditis elegans; Conjugation, Genetic; DNA microarrays; Drosophila melanogaster; E coli; Escherichia coli; Escherichia coli - genetics; Genetic regulation; Genetics; Genome, Bacterial; Life Sciences; Molecular biology; Mutants; Mutation; Oligonucleotide Array Sequence Analysis; Proteomics; Research methodology; Saccharomyces cerevisiae; Schizosaccharomyces pombe; United States
• ISSN: 1548-7091; 1548-7105
• DOI: 10.1038/nmeth.1239

An array-based high-throughput approach termed
Escherichia coli
synthetic genetic array, or eSGA, now allows comprehensive genetic interaction screens in bacteria. The method makes use of bacterial conjugation and robotic technology to generate double mutants on a genome-wide scale. In this issue, another paper presents GIANT-coli, a very similar approach.
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.