A new logic for DNA engineering using recombination in Escherichia coli

A straightforward way to engineer DNA in E. coli using homologous recombination is described. The homologous recombination reaction uses RecE and RecT and is transferable between E. coli strains. Several target molecules were manipulated, including high copy plasmids, a large episome and the E. coli chromosome. Sequential steps of homologous or site-specific recombination were used to demonstrate a new logic for engineering DNA, unlimited by the disposition of restriction endonuclease cleavage sites or the size of the target DNA.

[1]  R Kuhn,et al.  Temporally and spatially regulated somatic mutagenesis in mice. , 1998, Nucleic acids research.

[2]  D. K. Willis,et al.  Genes of the RecE and RecF pathways of conjugational recombination in Escherichia coli. , 1984, Cold Spring Harbor symposia on quantitative biology.

[3]  W. Bender,et al.  Construction of large DNA segments in Escherichia coli. , 1989, Science.

[4]  C. Chu,et al.  Transcription of the Escherichia coli recE gene from a promoter in Tn5 and IS50 , 1994, Journal of bacteriology.

[5]  R. Kolodner,et al.  Homologous pairing proteins encoded by the Escherichia coii recE and recT genes , 1994, Molecular microbiology.

[6]  P. Angrand,et al.  Different thermostabilities of FLP and Cre recombinases: implications for applied site-specific recombination. , 1996, Nucleic acids research.

[7]  K. Murphy,et al.  Use of Bacteriophage λ Recombination Functions To Promote Gene Replacement in Escherichia coli , 1998, Journal of bacteriology.

[8]  A. Clark.  Progress toward a metabolic interpretation of genetic recombination of Escherichia coli and bacteriophage lambda. , 1974, Genetics.

[9]  A. Clark,et al.  Biochemical and genetic studies of recombination proficiency in Escherichia coli. II. Rec+ revertants caused by indirect suppression of rec- mutations. , 1970, Proceedings of the National Academy of Sciences of the United States of America.

[10]  K. Murphy,et al.  Lambda Gam protein inhibits the helicase and chi-stimulated recombination activities of Escherichia coli RecBCD enzyme , 1991, Journal of bacteriology.

[11]  S. Elledge,et al.  Site-directed insertion and deletion mutagenesis with cloned fragments in Escherichia coli , 1985, Journal of bacteriology.

[12]  P. Dabert,et al.  Gene replacement with linear DNA fragments in wild-type Escherichia coli: enhancement by Chi sites. , 1997, Genetics.

[13]  D. Tollervey,et al.  One-step PCR mediated strategy for the construction of conditionally expressed and epitope tagged yeast proteins. , 1996, Nucleic acids research.

[14]  Jack W. Szostak,et al.  The double-strand-break repair model for recombination , 1983, Cell.

[15]  B. Sauer.  Site-specific recombination: developments and applications. , 1994, Current opinion in biotechnology.

[16]  R. Kolodner,et al.  DNA Strand Invasion Promoted by Escherichia coli RecT Protein* , 1998, The Journal of Biological Chemistry.

[17]  K. Muniyappa,et al.  The homologous recombination system of phage lambda. Pairing activities of beta protein. , 1986, The Journal of biological chemistry.

[18]  K. Kinzler,et al.  In vivo cloning of PCR products in E. coli. , 1993, Nucleic acids research.

[19]  M. Sekiguchi,et al.  Mutations of temperature sensitivity in R plasmid pSC101 , 1977, Journal of bacteriology.

[20]  K. Kinzler,et al.  A simplified system for generating recombinant adenoviruses. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[21]  R. Kolodner,et al.  Effect of terminal non-homology on intramolecular recombination of linear plasmid substrates in Escherichia coli. , 1992, Journal of molecular biology.

[22]  R. Kolodner,et al.  Homologous pairing and strand exchange promoted by the Escherichia coli RecT protein. , 1994, Proceedings of the National Academy of Sciences of the United States of America.

[23]  A. C. Chang,et al.  Construction of biologically functional bacterial plasmids in vitro. , 1973, Proceedings of the National Academy of Sciences of the United States of America.

[24]  M. Perricaudet,et al.  Recombinational construction in Escherichia coli of infectious adenoviral genomes. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[25]  C. Amemiya,et al.  A new bacteriophage P1–derived vector for the propagation of large human DNA fragments , 1994, Nature Genetics.

[26]  M. Resnick.  The repair of double-strand breaks in DNA; a model involving recombination. , 1976, Journal of theoretical biology.

[27]  J M Pemberton,et al.  An improved suicide vector for construction of chromosomal insertion mutations in bacteria. , 1992, Gene.

[28]  I. Blomfield,et al.  Allelic exchange in Escherichia coli using the Bacillus subtilis sacB gene and a temperature‐sensitive pSC101 replicon , 1991, Molecular microbiology.

[29]  W. Hammerschmidt,et al.  Cloning and mutagenesis of a herpesvirus genome as an infectious bacterial artificial chromosome. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[30]  P. Seeburg,et al.  Rapid construction in yeast of complex targeting vectors for gene manipulation in the mouse. , 1996, Nucleic acids research.

[31]  M. Mehtali,et al.  Efficient generation of recombinant adenovirus vectors by homologous recombination in Escherichia coli , 1996, Journal of virology.

[32]  B. Hohn,et al.  Cosmids: a type of plasmid gene-cloning vector that is packageable in vitro in bacteriophage lambda heads. , 1978, Proceedings of the National Academy of Sciences of the United States of America.

[33]  N. Heintz,et al.  Homologous recombination based modification in Esherichia coli and germline transmission in transgenic mice of a bacterial artificial chromsome , 1997, Nature Biotechnology.

[34]  B. Washburn,et al.  New method for generating deletions and gene replacements in Escherichia coli , 1989, Journal of bacteriology.

[35]  J. Murray,et al.  Site-specific recombinases: tools for genome engineering. , 1993, Trends in genetics : TIG.

[36]  F. Dahlquist,et al.  Chromosomal transformation of Escherichia coli recD strains with linearized plasmids , 1989, Journal of bacteriology.

[37]  N. Sternberg,et al.  Bacteriophage P1 cloning system for the isolation, amplification, and recovery of DNA fragments as large as 100 kilobase pairs. , 1990, Proceedings of the National Academy of Sciences of the United States of America.

[38]  Henry A. Erlich,et al.  Enzymatic amplification of ?-globin genomic sequences and restriction site analysis for diagnosis of , 1985 .

[39]  P. Angrand,et al.  A simple assay to determine the functionality of Cre or FLP recombination targets in genomic manipulation constructs. , 1996, Nucleic acids research.

[40]  R. Kolodner,et al.  Identification and Characterization of the Escherichia coli RecT Protein, a Protein Encoded by the recE Region That Promotes Renaturation of Homologous Single-Stranded DNA , 1993, Journal of bacteriology.

[41]  K. Mullis,et al.  Enzymatic amplification of beta-globin genomic sequences and restriction site analysis for diagnosis of sickle cell anemia. , 1985, Science.

[42]  B. Birren,et al.  Cloning and stable maintenance of 300-kilobase-pair fragments of human DNA in Escherichia coli using an F-factor-based vector. , 1992, Proceedings of the National Academy of Sciences of the United States of America.

[43]  B. Paw,et al.  Modification of bacterial artificial chromosomes through chi-stimulated homologous recombination and its application in zebrafish transgenesis. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[44]  O. Ozier-Kalogeropoulos,et al.  A simple and efficient method for direct gene deletion in Saccharomyces cerevisiae. , 1993, Nucleic acids research.

[45]  I. Kobayashi,et al.  Involvement of RecE exonuclease and RecT annealing protein in DNA double-strand break repair by homologous recombination. , 1994, Gene.

[46]  E. Degryse.  In vivo intermolecular recombination in Escherichia coli: application to plasmid constructions. , 1996, Gene.

[47]  P. Schimmel,et al.  Deletion of an essential gene in Escherichia coli by site-specific recombination with linear DNA fragments , 1984, Journal of bacteriology.

[48]  G. Church,et al.  Methods for generating precise deletions and insertions in the genome of wild-type Escherichia coli: application to open reading frame characterization , 1997, Journal of bacteriology.

[49]  W Bautsch,et al.  Rapid cloning by homologous recombination in vivo. , 1993, Nucleic acids research.