Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection

By T. Baba, Takeshi Ara, Miki Hasegawa, Yuki Takai, Yoshiko Okumura, Miki Baba, K. Datsenko, Masaru Tomita, B. Wanner, Hirotada Mori. Molecular Systems Biology, 2006

8,212 citations recorded by the source corpus.

We have systematically made a set of precisely defined, single‐gene deletions of all nonessential genes in Escherichia coli K‐12. Open‐reading frame coding regions were replaced with a kanamycin cassette flanked by FLP recognition target sites by using a one‐step method for inactivation of chromosomal genes and primers designed to create in‐frame deletions upon excision of the resistance cassette. Of 4288 genes targeted, mutants were obtained for 3985. To alleviate problems encountered in high‐throughput studies, two independent mutants were saved for every deleted gene. These mutants—the ‘Keio collection’—provide a new resource not only for systematic analyses of unknown gene functions and gene regulatory networks but also for genome‐wide testing of mutational effects in a common strain background, E. coli K‐12 BW25113. We were unable to disrupt 303 genes, including 37 of unknown function, which are candidates for essential genes. Distribution is being handled via GenoBase (http://ecoli.aist‐nara.ac.jp/).

Subfields: Genetics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/fc24f79df5adba19fab06e51de5f59aa40afe697

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Citations in the corpus

A white-box machine learning approach for revealing antibiotic mechanisms of action (2019, positive): “coli ΔglyA, ΔpurD, ΔpurE, ΔpurK, ΔpurM, ΔpurC and ΔpyrE gene deletion mutants were constructed by P1 phage transduction using the Keio collection (Baba et al., 2006), as previously described (Gutierrez et al.”
Ciprofloxacin Causes Persister Formation by Inducing the TisB toxin in Escherichia coli (2010, methodology): “P1 transduction was used to move the delta recA::Kan, delta sulA::Kan alleles (from the MORI KEIO collection [24]) and lexA300(Def) (kindly provided by G.”
Constraint-based models predict metabolic and associated cellular functions (2014, methodology): “Gene essentiality predictions were validated by comparison with a gene deletion collection 46 .”
Condition-Dependent Cell Volume and Concentration of Escherichia coli to Facilitate Data Conversion for Systems Biology Modeling (2011, methodology): “commonly used K-12 strain in several systems biology programs [7,19,20], when grown under 22 different growth conditions.”
Lysine succinylation is a frequently occurring modification in prokaryotes and eukaryotes and extensively overlaps with acetylation. (2013, methodology): “coli and Yeast Wild-type BW25113 and isogenic mutant cobBD (JW1106) strains (Baba et al., 2006) were obtained from the E.”
Phenotypic Landscape of a Bacterial Cell (2010, neutral): “coli have robust reported growth phenotypes, and only 8% of the genes are essential in rich media (Baba et al., 2006; Yamamoto et al., 2009).”