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Enyeart PJ, Chirieleison SM, Dao MN, Perutka J, Quandt EM, Yao J, Whitt JT, Keatinge-Clay AT, Lambowitz AM, Ellington AD. Generalized bacterial genome editing using mobile group II introns and Cre-lox. Mol Syst Biol 2013; 9:685. [PMID: 24002656 PMCID: PMC3792343 DOI: 10.1038/msb.2013.41] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2013] [Accepted: 07/23/2013] [Indexed: 12/21/2022] Open
Abstract
Efficient bacterial genetic engineering approaches with broad-host applicability are rare. We combine two systems, mobile group II introns ('targetrons') and Cre/lox, which function efficiently in many different organisms, into a versatile platform we call GETR (Genome Editing via Targetrons and Recombinases). The introns deliver lox sites to specific genomic loci, enabling genomic manipulations. Efficiency is enhanced by adding flexibility to the RNA hairpins formed by the lox sites. We use the system for insertions, deletions, inversions, and one-step cut-and-paste operations. We demonstrate insertion of a 12-kb polyketide synthase operon into the lacZ gene of Escherichia coli, multiple simultaneous and sequential deletions of up to 120 kb in E. coli and Staphylococcus aureus, inversions of up to 1.2 Mb in E. coli and Bacillus subtilis, and one-step cut-and-pastes for translocating 120 kb of genomic sequence to a site 1.5 Mb away. We also demonstrate the simultaneous delivery of lox sites into multiple loci in the Shewanella oneidensis genome. No selectable markers need to be placed in the genome, and the efficiency of Cre-mediated manipulations typically approaches 100%.
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Affiliation(s)
- Peter J Enyeart
- Institute for Cell and Molecular Biology, University of Texas at Austin, Austin, TX, USA
| | - Steven M Chirieleison
- Department of Biomedical Engineering, University of Texas at Austin, Austin, TX, USA
| | - Mai N Dao
- Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, TX, USA
- Section of Molecular Genetics and Microbiology, School of Biological Sciences, University of Texas at Austin, Austin, TX, USA
| | - Jiri Perutka
- Institute for Cell and Molecular Biology, University of Texas at Austin, Austin, TX, USA
- Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, TX, USA
| | - Erik M Quandt
- Institute for Cell and Molecular Biology, University of Texas at Austin, Austin, TX, USA
| | - Jun Yao
- Institute for Cell and Molecular Biology, University of Texas at Austin, Austin, TX, USA
- Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, TX, USA
- Section of Molecular Genetics and Microbiology, School of Biological Sciences, University of Texas at Austin, Austin, TX, USA
| | - Jacob T Whitt
- Institute for Cell and Molecular Biology, University of Texas at Austin, Austin, TX, USA
- Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, TX, USA
- Section of Molecular Genetics and Microbiology, School of Biological Sciences, University of Texas at Austin, Austin, TX, USA
| | - Adrian T Keatinge-Clay
- Institute for Cell and Molecular Biology, University of Texas at Austin, Austin, TX, USA
- Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, TX, USA
| | - Alan M Lambowitz
- Institute for Cell and Molecular Biology, University of Texas at Austin, Austin, TX, USA
- Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, TX, USA
- Section of Molecular Genetics and Microbiology, School of Biological Sciences, University of Texas at Austin, Austin, TX, USA
| | - Andrew D Ellington
- Institute for Cell and Molecular Biology, University of Texas at Austin, Austin, TX, USA
- Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, TX, USA
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