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

doi:10.1038/msb4100050

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

University

Research output: Contribution to journal › Article › peer-review

5641 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 language	English
Article number	msb4100050
Pages (from-to)	2006.0008
Journal	Molecular systems biology
Volume	2
DOIs	https://doi.org/10.1038/msb4100050
Publication status	Published - 2006 May 16

Keywords

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

ASJC Scopus subject areas

Biochemistry, Genetics and Molecular Biology(all)
Immunology and Microbiology(all)
Agricultural and Biological Sciences(all)
Applied Mathematics

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10.1038/msb4100050

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

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/).",

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author = "Tomoya Baba and Takeshi Ara and Miki Hasegawa and Yuki Takai and Yoshiko Okumura and Miki Baba and Datsenko, {Kirill A.} and Masaru Tomita and Wanner, {Barry L.} and Hirotada Mori",

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doi = "10.1038/msb4100050",

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AU - Takai, Yuki

AU - Okumura, Yoshiko

AU - Baba, Miki

AU - Datsenko, Kirill A.

AU - Tomita, Masaru

AU - Wanner, Barry L.

AU - Mori, Hirotada

PY - 2006/5/16

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

Abstract

Keywords

ASJC Scopus subject areas

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