title: A simple and effective method for construction of Escherichia coli strains proficient for genome engineering.
abstract: Multiplex genome engineering is a standalone recombineering tool for large-scale programming and accelerated evolution of cells. However, this advanced genome engineering technique has been limited to use in selected bacterial strains. We developed a simple and effective strain-independent method for effective genome engineering in Escherichia coli. The method involves introducing a suicide plasmid carrying the λ Red recombination system into the mutS gene. The suicide plasmid can be excised from the chromosome via selection in the absence of antibiotics, thus allowing transient inactivation of the mismatch repair system during genome engineering. In addition, we developed another suicide plasmid that enables integration of large DNA fragments into the lacZ genomic locus. These features enable this system to be applied in the exploitation of the benefits of genome engineering in synthetic biology, as well as the metabolic engineering of different strains of E. coli.
authors.affiliation: School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea.
authors.forename: Young Shin
authors.initials: YS
authors.lastname: Ryu
authors.affiliation: School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea.
authors.forename: Rajesh Kumar
authors.initials: RK
authors.lastname: Biswas
authors.affiliation: School of Biological Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea.
authors.forename: Kwangsu
authors.initials: K
authors.lastname: Shin
authors.affiliation: School of Biological Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea.
authors.forename: Vinuselvi
authors.initials: V
authors.lastname: Parisutham
authors.affiliation: School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea.
authors.forename: Suk Min
authors.initials: SM
authors.lastname: Kim
authors.affiliation: School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea; School of Biological Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea.
authors.forename: Sung Kuk
authors.initials: SK
authors.lastname: Lee
mesh_terms: D004926:Escherichia coli / Q000235:genetics* / Q000378:metabolism; D005818:Genetic Engineering / Q000379:methods*; D016680:Genome, Bacterial / Q000235:genetics*; D010957:Plasmids / Q000235:genetics; D014994:Xylose / Q000031:analogs & derivatives / Q000096:biosynthesis
chemical_list: C492551:deoxyxylulose phosphate; D014994:Xylose
references.citation: Science. 2011 Jul 15;333(6040):348-53
references.pmid: 21764749
references.citation: BMC Biotechnol. 2003 Jul 18;3:9
references.pmid: 12871598
references.citation: ACS Synth Biol. 2012 Feb 17;1(2):43-52
references.pmid: 22737598
references.citation: Appl Environ Microbiol. 2012 Jul;78(14):4984-94
references.pmid: 22582061
references.citation: Nucleic Acids Res. 2011 Sep 1;39(16):7336-47
references.pmid: 21609953
references.citation: Proc Natl Acad Sci U S A. 2000 May 23;97(11):5978-83
references.pmid: 10811905
references.citation: Gene. 2006 Sep 1;379:109-15
references.pmid: 16750601
references.citation: Proc Natl Acad Sci U S A. 2012 Jun 26;109(26):10540-5
references.pmid: 22689973
references.citation: Gene. 2001 Jul 11;272(1-2):227-35
references.pmid: 11470529
references.citation: J Bacteriol. 2008 Apr;190(7):2597-606
references.pmid: 18245285
references.citation: Mol Syst Biol. 2013;9:641
references.pmid: 23340847
references.citation: Nat Methods. 2012 Jun;9(6):591-3
references.pmid: 22484848
references.citation: Plasmid. 1996 Jan;35(1):1-13
references.pmid: 8693022
references.citation: Methods Enzymol. 2011;498:409-26
references.pmid: 21601688
references.citation: Bioeng Bugs. 2010 Jul-Aug;1(4):263-6
references.pmid: 21327058
references.citation: Appl Environ Microbiol. 2004 Nov;70(11):6887-91
references.pmid: 15528558
references.citation: Mutat Res. 2010 Oct;705(2):71-76
references.pmid: 20471491
references.citation: Nucleic Acids Res. 2008 May;36(9):e54
references.pmid: 18424799
references.citation: Gene. 2003 Oct 2;315:63-9
references.pmid: 14557065
references.citation: PLoS One. 2012;7(9):e44638
references.pmid: 22957093
references.citation: PLoS One. 2008 Jul 30;3(7):e2815
references.pmid: 18665232
references.citation: Genetics. 2010 Nov;186(3):791-9
references.pmid: 20813883
references.citation: Appl Microbiol Biotechnol. 2011 Feb;89(3):573-83
references.pmid: 21052988
references.citation: J Mol Biol. 2002 Nov 22;324(2):297-307
references.pmid: 12441108
references.citation: Methods Mol Biol. 2012;852:51-9
references.pmid: 22328425
references.citation: Proc Natl Acad Sci U S A. 2001 Jun 5;98(12):6765-70
references.pmid: 11381137
references.citation: Appl Environ Microbiol. 2012 Aug;78(15):5440-3
references.pmid: 22610439
references.citation: Nature. 2009 Aug 13;460(7257):894-898
references.pmid: 19633652
references.citation: Biotechniques. 1999 May;26(5):824-6, 828
references.pmid: 10337469
references.citation: Biotechnol Bioeng. 2005 Sep 5;91(5):636-42
references.pmid: 15898075