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

Tomoya Baba, Takeshi Ara, Miki Hasegawa, Yuki Takai, Yoshiko Okumura, Miki Baba, Kirill A. Datsenko, Masaru Tomita, Barry L. Wanner, Hirotada Mori

Research output: Contribution to journalArticle

3919 Citations (Scopus)

Abstract

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/).

Original languageEnglish
Article numbermsb4100050
JournalMolecular Systems Biology
Volume2
DOIs
Publication statusPublished - 2006 May 16

Fingerprint

Escherichia coli K12
Gene Knockout Techniques
knockout mutants
gene targeting
Mutant
Escherichia coli
Escherichia Coli
Genes
Gene
genes
mutants
Kanamycin
Deletion
Gene Regulatory Networks
Essential Genes
Gene Deletion
Gene Silencing
gene deletion
Open Reading Frames
kanamycin

Keywords

  • Bacterial functional genomics
  • E. coli/gene
  • Essential gene
  • Knockout mutants
  • Resources
  • Systems biology

ASJC Scopus subject areas

  • Medicine(all)
  • Immunology and Microbiology(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Agricultural and Biological Sciences(all)
  • Computational Theory and Mathematics
  • Information Systems
  • Applied Mathematics

Cite this

Baba, T., Ara, T., Hasegawa, M., Takai, Y., Okumura, Y., Baba, M., ... Mori, H. (2006). Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: The Keio collection. Molecular Systems Biology, 2, [msb4100050]. https://doi.org/10.1038/msb4100050

Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants : The Keio collection. / Baba, Tomoya; Ara, Takeshi; Hasegawa, Miki; Takai, Yuki; Okumura, Yoshiko; Baba, Miki; Datsenko, Kirill A.; Tomita, Masaru; Wanner, Barry L.; Mori, Hirotada.

In: Molecular Systems Biology, Vol. 2, msb4100050, 16.05.2006.

Research output: Contribution to journalArticle

Baba, T, Ara, T, Hasegawa, M, Takai, Y, Okumura, Y, Baba, M, Datsenko, KA, Tomita, M, Wanner, BL & Mori, H 2006, 'Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: The Keio collection', Molecular Systems Biology, vol. 2, msb4100050. https://doi.org/10.1038/msb4100050
Baba, Tomoya ; Ara, Takeshi ; Hasegawa, Miki ; Takai, Yuki ; Okumura, Yoshiko ; Baba, Miki ; Datsenko, Kirill A. ; Tomita, Masaru ; Wanner, Barry L. ; Mori, Hirotada. / Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants : The Keio collection. In: Molecular Systems Biology. 2006 ; Vol. 2.
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