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Abstract
Lambda Red recombineering is an easy and efficient method for generating genetic modifications in Escherichia coli. For gene deletions, lambda Red recombineering is combined with the use of selectable markers, which are removed through the action of, e.g., flippase (Flp) recombinase. This PCR-based engineering method has also been applied to a number of other bacteria. In this chapter, we describe a recently developed one plasmid-based method as well as the use of a strain with genomically integrated recombineering genes, which significantly speeds up the engineering of strains with multiple genomic alterations.
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Affiliation(s)
- Sheila Ingemann Jensen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark.
| | - Alex Toftgaard Nielsen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark.
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2
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Dubois V, Debreyer C, Litvak S, Quentin C, Parissi V. A new in vitro strand transfer assay for monitoring bacterial class 1 integron recombinase IntI1 activity. PLoS One 2007; 2:e1315. [PMID: 18091989 PMCID: PMC2117344 DOI: 10.1371/journal.pone.0001315] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2007] [Accepted: 11/21/2007] [Indexed: 11/19/2022] Open
Abstract
IntI1 integrase is a tyrosine recombinase involved in the mobility of antibiotic resistance gene cassettes within bacterial class 1 integrons. Recent data have shown that its recombination specifically involves the bottom strand of the attC site, but the exact mechanism of the reaction is still unclear. An efficient in vitro assay is still required to better characterize the biochemical properties of the enzyme. In this report we describe for the first time an in vitro system partially reproducing the activity of a recombinant pure IntI1. This new assay, which constitutes the only available in vitro model of recombination by IntI1, was used to determine whether this enzyme might be the sole bacterial protein required for the recombination process. Results show that IntI1 possesses all the features needed for performing recombination between attI and attC sites. However, differences in the in vitro intermolecular recombination efficiencies were found according to the target sites and were correlated with DNA affinities of the enzyme but not with in vivo data. The differential affinity of the enzyme for each site, its capacity to bind to a single-stranded structure at the attC site and the recombination observed with single-stranded substrates unambiguously confirm that it constitutes an important intermediary in the reaction. Our data strongly suggest that the enzyme possesses all the functions for generating and/or recognizing this structure even in the absence of other cellular factors. Furthermore, the in vitro assay reported here constitutes a powerful tool for the analysis of the recombination steps catalyzed by IntI1, its structure-function studies and the search for specific inhibitors.
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Affiliation(s)
- Véronique Dubois
- Laboratory of Cellular and Molecular Microbiology and Pathogenicity (MCMP), UMR 5097-CNRS, University Victor Segalen Bordeaux 2, Bordeaux, France
| | - Carole Debreyer
- Laboratory of Cellular and Molecular Microbiology and Pathogenicity (MCMP), UMR 5097-CNRS, University Victor Segalen Bordeaux 2, Bordeaux, France
| | - Simon Litvak
- Laboratory of Cellular and Molecular Microbiology and Pathogenicity (MCMP), UMR 5097-CNRS, University Victor Segalen Bordeaux 2, Bordeaux, France
| | - Claudine Quentin
- Laboratory of Cellular and Molecular Microbiology and Pathogenicity (MCMP), UMR 5097-CNRS, University Victor Segalen Bordeaux 2, Bordeaux, France
| | - Vincent Parissi
- Laboratory of Cellular and Molecular Microbiology and Pathogenicity (MCMP), UMR 5097-CNRS, University Victor Segalen Bordeaux 2, Bordeaux, France
- * To whom correspondence should be addressed. E-mail:
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3
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Abstract
Retrovirus-based vectors are presently the most efficient gene transfer vehicles for introducing genes into human hematopoietic stem and progenitor cells. However, their use for gene therapy is still problematic. A major obstacle is viral sequences such as the tRNA primer binding site or the dimerization and encapsidation signals that are not required for the expression of the therapeutic gene. These sequences can recombine with endogenous and/or exogenous retroviruses to generate new forms of unpredictable retroviruses. Moreover, these sequences are the targets for transcriptional repressors which inhibit the expression of the transduced genes. Therefore we have developed a new generation of retrovirus vectors which self-delete upon integration. The vectors are based on the natural life cycle of retroviruses, involving duplication of the terminal control regions U5 and U3 to generate long terminal repeats, and on the ability of the P1-phage site-specific recombinase (Cre) to excise any sequences positioned between two target sequences (loxP). Thus, while inserting a therapy gene into the genome, the vectors simultaneously excise most proviral sequences that are not required for gene expression.
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Affiliation(s)
- M Grez
- Laboratory for Molecular Virology, Georg-Speyer-Haus, Frankfurt, Germany
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4
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Abstract
The product topology of Xer-mediated site-specific recombination at plasmid sites has been determined. The product of deletion at pSC101 psi is a right-handed antiparallel 4-noded catenane. The ColE1 cer deletion product has an identical topology, except that only one pair of strands is exchanged. These specific product topologies imply that the productive synaptic complex and the strand exchange mechanism have fixed topologies. Further analysis suggests that synapsis traps exactly three negative supercoils between recombining sites, and that strand exchange introduces a further negative topological node in the deletion reaction. We present a model in which the requirement for a specific synaptic stucture, with two recombination sites interwrapped around the accessory proteins ArgR and PepA, ensures that recombination only occurs efficiently between directly repeated sites on the same DNA molecule.
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Affiliation(s)
- S D Colloms
- Department of Biochemistry, University of Oxford, United Kingdom
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5
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Sadowski PD. The Flp Recombinase of th 2-μm Plasmid of Saccharomyces cerevisiae. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 1995. [DOI: 10.1016/s0079-6603(08)60876-4] [Citation(s) in RCA: 114] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
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6
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Abstract
Site-specific DNA recombination systems have considerable utility in manipulating DNA and can facilitate many cloning and gene transfer techniques. The ability of a number of recombinases to catalyze efficient DNA recombination in higher eukaryotes has important and exciting consequences for precise chromosome and transgene engineering. Exploitation of these recombinases will facilitate the generation of transgenic animal disease models and help elucidate the function of developmental genes.
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Affiliation(s)
- B Sauer
- National Institute of Diabetes, Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892
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7
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Kulpa J, Dixon J, Pan G, Sadowski P. Mutations of the FLP recombinase gene that cause a deficiency in DNA bending and strand cleavage. J Biol Chem 1993. [DOI: 10.1016/s0021-9258(18)54047-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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8
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Schwartz CJ, Sadowski PD. FLP recombinase of the 2 microns circle plasmid of Saccharomyces cerevisiae bends its DNA target. Isolation of FLP mutants defective in DNA bending. J Mol Biol 1989; 205:647-58. [PMID: 2648010 DOI: 10.1016/0022-2836(89)90310-0] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The FLP recombinase is encoded by the yeast plasmid 2 microns circle and catalyses a site-specific recombination reaction that results in inversion of a segment of the 2 micron plasmid. We describe a method for the isolation of inactivating mutations in the FLP gene. The analysis of the recombination and binding activity of defective FLP proteins in vitro resulted in the identification of two classes of mutations: those that completely abolish FLP function by interfering with DNA binding and others that block recombination after the binding step. We have shown that FLP-mediated recombination is accompanied by bending of the DNA target and that mutations in the FLP recombinase that block bending also eliminate recombination.
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Affiliation(s)
- C J Schwartz
- Department of Medical Genetics, University of Toronto, Ontario, Canada
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9
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Rank GH, Arndt GM, Xiao W. FLP-FRT mediated intrachromosomal recombination on a tandemly duplicated YEp integrant at the ILV2 locus of chromosome XIII in Saccharomyces cerevisiae. Curr Genet 1989; 15:107-12. [PMID: 2663188 DOI: 10.1007/bf00435456] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
A YEp chimaeric plasmid carrying SMR1 and URA3 genetic markers was integrated into chromosome XIII at the ilv2-delta 1 locus in a [cir (o)] background. The 1.5 kb BglII deletion of ilv2-delta 1 allowed the clear identification of an integrant structure which consisted of a direct tandem duplication (TD) of the chimaeric plasmid. Within the integrant structure, a single copy of the plasmid sequence was flanked by a direct duplication of the 2 microns site-specific recombinase (FLP) recognition target (FRT). Isogenic [cir (o)] and [cir+] diploids formed by crossing the [cir (o)] TD strain to complementary haploids were analyzed for plasmid marker loss and chromosomal DNA alterations in the presence and absence of selection pressure for the URA3 and SMR1 plasmid borne markers. [cir (o)] diploids showed no plasmid marker loss and maintained the TD structure. In the absence of selection pressure, the [cir+] diploid underwent FLP-FRT mediated unequal interchromatid recombination, resulting in the breakage-fusion-bridge cycle and homozygotization of chromosome XIII (Rank et al. 1988). Maintenance of selection pressure for the centromere distal plasmid URA3 marker selected against FLP-FRT interchromatid recombinants so that the effects of site specific recombinase on intrachromatid recombination could be evaluated. Intrachromatid recombination at the directly duplicated FRT sites of the TD structure resulted in the loss of a diagnostic internal fragment. These results show that in the presence of FLP, FRT sites separated by up to 13.3 kb of chromosomal DNA function as substrates for intra and interchromatid recombination.
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Affiliation(s)
- G H Rank
- Department of Biology, University of Saskatchewan, Saskatoon, Canada
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10
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Affiliation(s)
- A B Futcher
- Department of Biochemistry, McMaster University, Hamilton, Ontario, Canada
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11
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Shepherd HS, Ligon JM, Bolen PL, Kurtzman CP. Cryptic DNA plasmids of the heterothallic yeast Saccharomycopsis crataegensis. Curr Genet 1987. [DOI: 10.1007/bf00435293] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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12
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Beatty LG, Babineau-Clary D, Hogrefe C, Sadowski PD. FLP site-specific recombinase of yeast 2-micron plasmid. Topological features of the reaction. J Mol Biol 1986; 188:529-44. [PMID: 3016286 DOI: 10.1016/s0022-2836(86)80003-1] [Citation(s) in RCA: 27] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The 2-micron plasmid of the yeast Saccharomyces cerevisiae encodes a site-specific recombinase (FLP) that promotes inversion across a unique site contained in each of the 599-base-pair inverted repeats of the plasmid. We have studied the topological changes generated in supercoiled substrates after exposure to the purified FLP protein in vitro. When a supercoiled substrate bearing two FLP target sequences in inverse orientation is treated with FLP, the products are multiply knotted structures that arise as a result of random entrapment of interdomainal supercoils. Likewise, a supercoiled substrate bearing two target sequences in direct orientation yields multiply interlocked catenanes as the product. Both types of substrate seem to be able to undergo repeated rounds of recombination that result in products of further complexity. The FLP protein also acts as a site-specific topoisomerase during the recombination reaction.
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14
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Andrews BJ, Beatty LG, Sadowski PD. Site-specific recombination of the yeast plasmid two-micron circle: intermediates in the binding process. BASIC LIFE SCIENCES 1986; 40:407-24. [PMID: 3551918 DOI: 10.1007/978-1-4684-5251-8_31] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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15
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Babineau D, Vetter D, Andrews BJ, Gronostajski RM, Proteau GA, Beatty LG, Sadowski PD. The FLP protein of the 2-micron plasmid of yeast. Purification of the protein from Escherichia coli cells expressing the cloned FLP gene. J Biol Chem 1985. [DOI: 10.1016/s0021-9258(17)39027-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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16
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Gronostajski RM, Sadowski PD. Determination of DNA sequences essential for FLP-mediated recombination by a novel method. J Biol Chem 1985. [DOI: 10.1016/s0021-9258(17)39028-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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