Precise manipulation of bacterial chromosomes by conjugative assembly genome engineering

Nature Protocols

Volumn 9, Issue 10, 2014, Pages 2285-2300

  Ma, Natalie J ^a   Moonan, Daniel W ^a   Isaacs, Farren J ^a  

^a YALE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BACTERIAL CHROMOSOME; BACTERIAL GENETICS; BACTERIAL STRAIN; BACTERIUM CONJUGATION; CHIMERA; CONJUGATIVE ASSEMBLY GENOME ENGINEERING; CONTROLLED STUDY; ESCHERICHIA COLI; GENE TRANSFER; GENETIC ENGINEERING; IN VITRO STUDY; NONHUMAN; PRIORITY JOURNAL; BACTERIAL GENOME; GENETIC MARKER; GENETICS; GENOMICS; PLASMID; PROCEDURES;

BACTERIA (MICROORGANISMS); ESCHERICHIA COLI;

GENETIC MARKER;

CHROMOSOMES, BACTERIAL; CONJUGATION, GENETIC; ESCHERICHIA COLI; GENETIC MARKERS; GENOME, BACTERIAL; GENOMICS; PLASMIDS;

EID: 84926003341     PISSN: 17542189     EISSN: 17502799     Source Type: Journal    
DOI: 10.1038/nprot.2014.081     Document Type: Article

References (24)

1. Ochman, H., Lawrence, J.G. & Groisman, E.A. Lateral gene transfer and the nature of bacterial innovation. Nature 405, 299-304 (2000).
2. Smith, G.R. Conjugational recombination in E. coli: myths and mechanisms. Cell 64, 19-27 (1991).
3. Lederberg, J. & Tatum, E. Gene recombination in Escherichia coli. Nature 53, 673-684 (1946).
4. Pansegrau, W. et al. Complete nucleotide sequence of Birmingham IncPα plasmids: compilation and comparative analysis. J. Mol. Biol. 239, 623-663 (1994).
5. Lanka, E. & Wilkins, B.M. DNA processing reactions in bacterial conjugation. Annu. Rev. Biochem. 64, 141-169 (1995).
6. Curtiss, R. Bacterial conjugation. Annu. Rev. Microbiol. 23, 69-136 (1969).
7. Fürste, J. & Pansegrau, W. Conjugative transfer of promiscuous IncP plasmids: interaction of plasmid-encoded products with the transfer origin. Proc. Natl. Acad. Sci. USA 86, 1771-1775 (1989).
8. Guiney, D. & Yakobson, E. Location and nucleotide sequence of the transfer origin of the broad host range plasmid RK2. Proc. Natl. Acad. Sci. USA 80, 3595-3598 (1983).
9. Wollman, E.-L., Jacob, F. & Hayes, W. Conjugation and genetic recombination in Escherichia coli K-12. Cold Spring Harb. Symp. Quant. Biol. 21, 141-162 (1956).
10. Isaacs, F.J. et al. Precise manipulation of chromosomes in vivo enables genome-wide codon replacement. Science 333, 348-353 (2011).
11. Court, D.L., Sawitzke, J.A. & Thomason, L.C. Genetic engineering using homologous recombination. Annu. Rev. Genet. 36, 361-388 (2002).
12. Sharan, S.K., Thomason, L.C., Kuznetsov, S.G. & Court, D.L. Recombineering: a homologous recombination-based method of genetic engineering. Nat. Protoc. 4, 206-223 (2009).
13. DeVito, J.A. Recombineering with tolC as a selectable/counter-selectable marker: remodeling the rRNA operons of Escherichia coli. Nucleic Acids Res. 36, e4 (2008).
14. Schwartz, S.A. & Helinski, D.R. Purification and characterization of colicin E1. J. Biol. Chem. 246, 6318-6327 (1971).
15. Gallagher, R.R., Li, Z., Lewis, A.O. & Isaacs, F.J. Nat. Protoc. 9, 2301-2316 (2014).
16. Lajoie, M.J. et al. Genomically recoded organisms expand biological functions. Science 342, 357-360 (2013).
17. Bates, S., Cashmore, A.M. & Wilkins, B.M. IncP plasmids are unusually effective in mediating conjugation of Escherichia coli and Saccharomyces cerevisiae: involvement of the Tra2 mating system. J. Bacteriol. 180, 6538-6543 (1998).
18. Thomas, C.M. & Smith, C.A. Incompatibility group P plasmids: genetics, evolution, and use in genetic manipulation. Annu. Rev. Microbiol. 41, 77-101 (1987).
19. Waters, V.L. Conjugation between bacterial and mammalian cells. Nat. Genet. 231, 375-376 (2001).
20. Gregg, C.J. et al. Rational optimization of tolC as a powerful dual selectable marker for genome engineering. Nucleic Acids Res. 42, 4779-4790 (2014).
21. Smith, C., Econome, J. & Schutt, A. A physical map of the Escherichia coli K 12 genome. Science 236, 1448-1453 (1987).
22. Warming, S., Costantino, N., Court, D.L., Jenkins, N.A. & Copeland, N.G. Simple and highly efficient BAC recombineering using galK selection. Nucleic Acids Res. 33, e36 (2005).
23. Wong, Q.N.Y. et al. Efficient and seamless DNA recombineering using a thymidylate synthase A selection system in Escherichia coli. Nucleic Acids Res. 33, e59 (2005).
24. SantaLucia, J. A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics. Proc. Natl. Acad. Sci. USA 95, 1460-1465 (1998).