Minimization of the Escherichia coli genome using a Tn5-targeted Cre/IoxP excision system

Nature Biotechnology

Volumn 20, Issue 10, 2002, Pages 1018-1023

  Yu, Byung Jo ^a   Sung, Bong Hyun ^a   Koob, Michael D ^b   Lee, Choong Hoon ^a   Lee, Jun Hyoung ^a   Lee, Won Sik ^a   Kim, Mi Sun ^c   Kim, Sun Chang ^a  

^a Korea Advanced Institute of Science and Technology (KAIST)   (South Korea)

^b UNIVERSITY OF MINNESOTA   (United States)

^c Korea Institute of Energy Research (KIER)   (South Korea)

Author keywords

[No Author keywords available]

Indexed keywords

BIOMARKERS; ESCHERICHIA COLI; MUTAGENESIS;

EXCISION SYSTEMS;

GENES;

ARTICLE; BACTERIAL GENOME; BACTERIAL STRAIN; CONTROLLED STUDY; ESCHERICHIA COLI; EXCISION; GENE SEQUENCE; GENE TARGETING; GENETIC ENGINEERING; MUTANT; NONHUMAN; OPEN READING FRAME; PRIORITY JOURNAL; STANDARD; TRANSPOSON;

BACTERIOPHAGE P1; CELL LINE; CHROMOSOMES, BACTERIAL; CLONING, MOLECULAR; DNA TRANSPOSABLE ELEMENTS; ESCHERICHIA COLI; GENE DELETION; GENETIC ENGINEERING; GENOME, BACTERIAL; INTEGRASES; MUTAGENESIS; RECOMBINATION, GENETIC; REPLICATION ORIGIN; SPECIES SPECIFICITY; TRANSDUCTION, GENETIC; VIRAL PROTEINS;

BACTERIA (MICROORGANISMS); ESCHERICHIA COLI; NEGIBACTERIA; PROKARYOTA; TRANSPOSONS;

EID: 0036787648     PISSN: 10870156     EISSN: None     Source Type: Journal    
DOI: 10.1038/nbt740     Document Type: Article

References (24)

1. Schmid, M.B., Kapur, N., Isaacson, D.R., Lindroos, P. & Sharpe, C. Genetic analysis of temperature-sensitive lethal mutants of Salmonella typhimurium. Genetics 123, 625-663 (1989).
2. Arigoni, F. et al. A genome-based approach for the identification of essential bacterial genes. Nat. Biotechnol. 16, 851-856 (1998).
3. Mushegian, A.R. & Koonin, E.V. A minimal gene set for cellular life derived by comparison of complete bacterial genomes. Proc. Natl. Acad. Sci. USA 93, 10268-10273 (1996).
4. Winzeler, E.A. et al. Functional characterization of the S. Cerevisiae genome by gene deletion and parallel analysis. Science 285, 901-906 (1999).
5. Itaya, M. An estimation of minimal genome size required for life. FEBS Lett. 362, 257-260 (1995).
6. Akerley, B.J. et al. A genome-scale analysis for identification of genes required for growth or survival of Haemophilus influenzae. Proc. Natl. Acad. Sci. USA 99, 966-971 (2002).
7. Blattner, F.R. et al. The complete genome sequence of Escherichia coli K-12. Science 277, 1453-1474 (1997).
8. Tao, H., Bausch, C., Richmond, C., Blattner, F.R. & Conway, T. Functional genomics: expression analysis of Escherichia coli growing on minimal and rich media. J. Bacteriol. 181, 6425-6440 (1999).
9. Koob, M.D., Shaw, A.J. & Cameron, D.C. Minimizing the genome of Escherichia coli. Ann. N. Y. Acad. Sci. 745, 1-3 (1994).
10. Yoon, Y.G., Cho, J.H. & Kim, S.C. Cre/loxP-mediated excision and amplification of the Escherichia coli genome. Genet. Anal. 14, 89-95 (1998).
11. Datsenko, K.A. & Wanner, B.L. One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products. Proc. Natl. Acad. Sci. USA 97, 6640-6645 (2000).
12. Posfai, G. et al. In vivo excision and amplification of large segments of the Escherichia coli genome. Nucleic Acids Res. 22, 2392-2398 (1994).
13. Hasan, N., Koob, M. & Szybalski, W. Escherichia coli genome targeting, I. Crelox-mediated in vitro generation of ori- plasmids and their in vivo chromosomal integration and retrieval. Gene 150, 51-56 (1994).
14. Kolisnychenko, V. et al. Engineering a reduced Escherichia coligenome. Genome Res. 12, 640-647 (2002).
15. Szybalski, W. From the double-helix to novel approaches to the sequencing of large genomes. Gene 135, 279-290 (1993).
16. Pratt, L.A. & Kolter, R. Genetic analysis of Echerichia coli biofilm formation: roles of flagella, motility, chemotaxis and type I pill. Mol. Microbiol. 30, 285-293 (1998).
17. Lawrence, J.G. & Ochman, H. Molecular archaeology of the Escherichia coli genome. Proc. Natl. Acad. Sci. USA 95, 9413-9417 (1998).
18. 3 molecular weight plasmid-encoded protein is required for replication and copy number control in the plasmid pSC101 and its temperature-sensitive derivatives pHS1. J. MoL Biol. 175, 331-348 (1984).
19. Thompson, J.R., Register, E., Curotto, J., Kurtz, M. & Kelly, R. An improved protocol for the preparation of yeast cells for transformation by electroporation. Yeast 14, 565-571 (1998).
20. Grant, S.G., Jessee, J., Bloom, F.R. & Hanahan, D. Differential plasmid rescue from transgenic mouse DNAs into Escherichia coli methylation-restriction mutants. Proc. Natl. Acad. Sci. USA 87, 4645-4649 (1990).
21. Goryshin, I.Y., Jendrisak, J., Hoffman, L.M., Mels, R. & Reznikoff, W.S. Insertional transposon mutagenesis by electroporation of released Tn5 transposition complexes. Nat. Biotechnol. 18, 97-100 (2000).
22. Sambrook, J. & Russell, D.W. Molecular Cloning: A Laboratory Manual, Edn. 3 (Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, 2001).
23. Altschul, S.F., Gish, W., Miller, W., Myers, E.W. & Lipman, D.J. Basic local alignment search tool. J. Mol. Biol. 215, 403-410 (1990).
24. Miller, J.H. A Short Course in Bacterial Genetics: A Laboratory Manual and Handbook for Escherichia coli and Related Bacteria (Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York, 1992).