A highly sensitive selection method for directed evolution of homing endonucleases

Nucleic Acids Research

Volumn 33, Issue 18, 2005, Pages 1-7

  Chen, Zhilei ^a   Zhao, Huimin ^a,b  

^a UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

^b University of Illinois at Urbana Champaign   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DEOXYRIBONUCLEASE; DOUBLE STRANDED DNA; ENDONUCLEASE I SCEI; HOMING ENDONUCLEASE; UNCLASSIFIED DRUG; ENDODEOXYRIBONUCLEASE SCEI; TYPE II SITE SPECIFIC DEOXYRIBONUCLEASE;

ARTICLE; CELL SURVIVAL; DIRECTED MOLECULAR EVOLUTION; DNA CLEAVAGE; DNA RECOMBINATION; ENZYME ANALYSIS; ENZYME MECHANISM; ESCHERICHIA COLI; GENE THERAPY; METHODOLOGY; NONHUMAN; PRIORITY JOURNAL; WILD TYPE; BACTERIUM TRANSFORMATION; ENZYME SPECIFICITY; EVALUATION; GENETICS; METABOLISM; PLASMID;

ESCHERICHIA COLI;

DEOXYRIBONUCLEASES, TYPE II SITE-SPECIFIC; DIRECTED MOLECULAR EVOLUTION; ENDODEOXYRIBONUCLEASES; ESCHERICHIA COLI; PLASMIDS; SUBSTRATE SPECIFICITY; TRANSFORMATION, BACTERIAL;

EID: 28544437131     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gni148     Document Type: Article

References (31)

1. Belfort,M. and Roberts,R.J. (1997) Homing endonucleases: Keeping the house in order. Nucleic Acids Res., 25, 3379-3388.
2. Szostak,J.W., Orr-Weaver,T.L., Rothstein,R.J. and Stahl,F.W. (1983) The double-strand-break repair model for recombination. Cell, 33, 25-35.
3. Jasin,M. (1996) Genetic manipulation of genomes with rare-cutting endonucleases. Trends Genet., 12, 224-228.
4. Cohen-Tannoudji,M., Robine,S., Choulika,A., Pinto,D., El Marjou,F., Babinet,C., Louvard,D. and Jaisser,F. (1998) I-SceI-induced gene replacement at a natural locus in embryonic stem cells. Mol. Cell. Biol., 18, 1444-1448.
5. Gimble,F.S., Moure,C.M. and Posey,K.L. (2003) Assessing the plasticity of DNA target site recognition of the PI-SceI homing endonuclease using a bacterial two-hybrid selection system. J. Mol. Biol., 334, 993-1008.
6. Seligman,L.M., Chisholm,K.M., Chevalier,B.S., Chadsey,M.S., Edwards,S.T., Savage,J.H. and Veillet,A.L. (2002) Mutations altering the cleavage specificity of a homing endonuclease. Nucleic Acids Res., 30, 3870-3879.
7. Sussman,D., Chadsey,M., Fauce,S., Engel,A., Bruett,A., Monnat,R.,Jr, Stoddard,B.L. and Seligman,L.M. (2004) Isolation and characterization of new homing endonuclease specificities at individual target site positions. J. Mol. Biol., 342, 31-41.
8. Gruen,M., Chang,K., Serbanescu,I. and Liu,D.R. (2002) An in vivo selection system for homing endonuclease activity. Nucleic Acids Res., 30, e29.
9. Carrier,T., Jones,K.L. and Keasling,J.D. (1998) mRNA stability and plasmid copy number effects on gene expression from an inducible promoter system. Biotechnol. Bioeng., 59, 666-672.
10. Guzman,L.M., Belin,D., Carson,M.J. and Beckwith,J. (1995) Tight regulation, modulation, and high-level expression by vectors containing the arabinose PBAD promoter. J. Bacteriol., 177, 4121-4130.
11. Morgan-Kiss,R.M., Wadler,C. and Cronan,J.E.,Jr (2002) Long-term and homogeneous regulation of the Escherichia coli araBAD promoter by use of a lactose transporter of relaxed specificity. Proc. Natl Acad. Sci. USA, 99, 7373-7377.
12. Perrin,A., Buckle,M. and Dujon,B. (1993) Asymmetrical recognition and activity of the I-SceI endonuclease on its site and on intron-exon junctions. EMBO J., 12, 2939-2947.
13. Sarkar,G. and Sommer,S.S. (1990) The 'megaprimer' method of site-directed mutagenesis. Biotechniques, 8, 404-407.
14. Datsenko,K.A, and Wanner,B.L. (2000) One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products. Proc. Natl Acad. Sci. USA, 97, 6640-6645.
15. Lessard,I.A., Pratt,S.D., McCafferty,D.G., Bussiere,D.E., Hutchins,C., Wanner,B.L., Katz,L. and Walsh,C.T. (1998) Homologs of the vancomycin resistance D-Ala-D-Ala dipeptidase VanX in Streptomyces toyocaensis, Escherichia coli and Synechocystis: Attributes of catalytic efficiency, stereoselectivity and regulation with implications for function. Chem. Biol., 5, 489-504.
16. Dower,W.J., Miller,J.F. and Ragsdale,C.W. (1988) High efficiency transformation of E.coli by high voltage electroporation. Nucleic Acids Res., 16, 6127-6145.
17. Bahassi,E.M., Salmon,M.A., Van Melderen,L., Bernard,P. and Couturier,M. (1995) F plasmid ccdB killer protein: CcdB gene mutants coding for non-cytotoxic proteins which retain their regulatory functions. Mol. Microbiol., 15, 1031-1037.
18. Loris,R., Dao-Thi,M.H., Bahassi,E.M., Van Melderen,L., Poortmans,F., Liddington,R., Couturier,M. and Wyns,L. (1999) Crystal structure of CcdB, a topoisomerase poison from E.coli. J. Mol. Biol., 285, 1667-1677.
19. Kuzminov,A. and Stahl,F.W. (1997) Stability of linear DNA in recA mutant Escherichia coli cells reflects ongoing chromosomal DNA degradation. J. Bacteriol., 179, 880-888.
20. Colleaux,L., d'Auriol,L., Betermier,M., Cottarel,G., Jacquier,A., Galibert,F. and Dujon,B. (1986) Universal code equivalent of a yeast mitochondrial intron reading frame is expressed into E.coli as a specific double strand endonuclease. Cell, 44, 521-533.
21. Jacquier,A. and Dujon,B. (1985) An intron-encoded protein is active in a gene conversion process that spreads an intron into a mitochondrial gene. Cell, 41, 383-394.
22. Monteilhet,C., Perrin,A., Thierry,A., Colleaux,L. and Dujon,B. (1990) Purification and characterization of the in vitro activity of I-Sce I, a novel and highly specific endonucleese encoded by a group I intron. Nucleic Acids Res., 18, 1407-1413.
23. Moure,C.M., Gimble,F.S. and Quiocho,F.A. (2003) The crystal structure of the gene targeting homing endonuclease I-SceI reveals the origins of its target site specificity. J. Mol. Biol., 334, 685-695.
24. Smolke,C.D., Khlebnikov,A. and Keasling,J.D. (2001) Effects of transcription induction homogeneity and transcript stability on expression of two genes in a constructed operon. Appl. Microbiol. Biotechnol., 57, 689-696.
25. Siegele,D.A. and Hu,J.C. (1997) Gene expression from plasmids containing the araBAD promoter at subsaturating inducer concentrations represents mixed populations. Proc. Natl Acad. Sci. USA, 94, 8168-8172.
26. Novick,A. and Weiner,M. (1954) Enzyme induction as an all-or-none phenomenon. Proc. Natl Acad. Sci. USA, 43, 553-556.
27. Johnson,C.M. and Schleif,R.F. (1995) In vivo induction kinetics of the arabinose promoters in Escherichia coli. J. Bacteriol., 177, 3438-3442.
28. Haldimann,A., Daniels,L.L. and Wanner,B.L. (1998) Use of new methods for construction of tightly regulated arabinose and rhamnose promoter fusions in studies of the Escherichia coli phosphate regulon. J. Bacteriol., 180, 1277-1286.
29. Miyada,C.G., Stoltzfus,L. and Wilcox,G. (1984) Regulation of the araC gene of Escherichia coli: Catabolite repression, autoregulation, and effect on araBAD expression. Proc. Natl Acad. Sci. USA, 81, 4120-4124.
30. Carrier,T.A. and Keasling,J.D. (1997) Controlling messenger RNA stability in bacteria: Strategies for engineering gene expression. Biotechnol. Prog., 13, 699-708.
31. Reichmuth,D.S., Blanch,H.W. and Keasling,J.D. (2004) Dibenzothiophene biodesulfurization pathway improvement using diagnostic GFP fusions. Biotechnol. Bioeng., 88, 94-99.