Cre/lox system and PCR-based genome engineering in Bacillus subtilis

Applied and Environmental Microbiology

Volumn 74, Issue 17, 2008, Pages 5556-5562

  Yan, Xin ^a   Yu, Hao Jie ^a   Hong, Qing ^a   Li, Shun Peng ^a  

^a NANJING AGRICULTURAL UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTER NETWORKS;

BACILLUS SUBTILIS; IN-VIVO; INDUCIBLE EXPRESSION;

COSMIC RAYS;

CRE RECOMBINASE;

BACTERIUM; ENZYME ACTIVITY; GENE EXPRESSION; GENETIC ENGINEERING; GENOME; HOMOLOGY; POLYMERASE CHAIN REACTION;

ARTICLE; BACILLUS SUBTILIS; BACTERIAL GENOME; GENE CASSETTE; GENE DELETION; GENE INACTIVATION; GENE MUTATION; GENETIC ENGINEERING; GENETIC MANIPULATION; GENETIC RECOMBINATION; LOXP SITE; MARKER GENE; MUTAGENESIS; NONHUMAN; NUCLEOTIDE SEQUENCE; POLYMERASE CHAIN REACTION;

BACILLUS SUBTILIS; CHROMOSOMES, BACTERIAL; DNA, BACTERIAL; DNA, RECOMBINANT; GENETIC ENGINEERING; GENETIC VECTORS; GENOME, BACTERIAL; INTEGRASES; ISOPROPYL THIOGALACTOSIDE; MOLECULAR SEQUENCE DATA; ORGANISMS, GENETICALLY MODIFIED; PLASMIDS; POLYMERASE CHAIN REACTION;

BACILLUS SUBTILIS;

EID: 50949129295     PISSN: 00992240     EISSN: None     Source Type: Journal    
DOI: 10.1128/AEM.01156-08     Document Type: Article

References (40)

1. Abremski, K., R. Hoess, and N. Sternberg. 1983. Studies on the properties of P1 site-specific recombination: evidence for topologically unlinked products following recombination. Cell 32:1301-1311.
2. Albert, H., E. C. Dale, E. Lee, and D. W. Ow. 1995. Site-specific integration of DNA into wild-type and mutant lox sites placed in the plant genome. Plant J. 7:649-659.
3. Anagnostopoulos, C., and J. Spizizen. 1961. Requirements for transformation in Bacillus subtilis. J. Bacteriol. 81:741-746.
4. Baba, T., T. Ara, M. Hasegawa, Y. Takai, Y. Okumura, M. Baba, K. A. Datsenko, M. Tomita, B. L. Wanner, and H. Mori. 2006. Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection. Mol. Syst. Biol. 2:2006.0008. doi:10.1038/msb4100050.
5. Baudin, A., O. Ozier-Kalogeropoulos, A. Denouel, F. Lacroute, and C. Cullin. 1993. A simple and efficient method for direct gene deletion in Saccharomyces cerevisiae. Nucleic Acids Res. 21:3329-3330.
6. Brans, A., P. Filée, A. Chevigné, A. Claessens, and B. Joris. 2004. New integrative method to generate Bacillus subtilis recombinant strains free of selection markers. Appl. Environ. Microbiol. 70:7241-7250.
7. Broach, J. R., V. R. Guarascio, and M. Jayaram. 1982. Recombination within the yeast plasmid 2μ circle is site-specific. Cell 29:227-234.
8. Bron, S., R. Meima, J. M. van Dijl, A. Wipat, and C. Harwood. 1999. Molecular biology and genetics of Bacillus spp., p. 392-416. In A. L. Demain and J. E. Davies (ed.), Manual of industrial microbiology and biotechnology, 2nd ed. ASM Press, Washington, DC.
9. Cui, Z. L., X. Z. Zhang, Z. H. Zhang, and S. P. Li. 2004. Construction and application of a promoter-trapping vector with methyl parathion hydrolase gene mpd as the reporter. Biotechnol. Lett. 26:1115-1118.
10. Dahl, M. K., and C. G. Meinhof. 1994. A series of integrative plasmids for Bacillus subtilis containing unique cloning sites in all three open reading frames for translational lacZ fusions. Gene 145:151-152.
11. Datsenko, K. A., and B. L. Wanner. 2000. One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products. Proc. Natl. Acad. Sci. USA 97:6640-6645.
12. Defoor, E., M. B. Kryger, and J. Martinussen. 2007. The orotate transporter encoded by oroP from Lactococcus lactis is required for orotate utilization and has utility as a food-grade selectable marker. Microbiology 153:3645-3659.
13. Dempsey, L. A., and D. A. Dubnau. 1989. Localization of the replication origin of plasmid pE194. J. Bacteriol. 171:2866-2869.
14. Dubnau, D. 1991. Genetic competence in Bacillus subtilus. Microbiol. Rev. 55:395-424.
15. Dubnau, D. 1993. Genetic exchange and homologous recombination, p. 555-584. In A. L. Sonenshein, J. A. Hoch, and R. Losick (ed.), Bacillus subtilis and other gram-positive bacteria: biochemistry, physiology, and molecular genetics. American Society for Microbiology, Washington, DC.
16. Ellermeier, C. D., and R. Losick. 2006. Evidence for a novel protease governing regulated intramembrane proteolysis and resistance to antimicrobial peptides in Bacillus subtilis. Genes Dev. 20:1911-1922.
17. Fabret, C., S. D. Ehrlich, and P. Noirot. 2002. A new mutation delivery system for genome-scale approaches in Bacillus subtilis. Mol. Microbiol. 46:25-36.
18. Guerout-Fleury, A. M., K. Shazand, N. Frandsen, and P. Stragier. 1995. Antibiotic-resistance cassettes for Bacillus subtilis. Gene 167:335-336.
19. Härtl, B., W. Wehrl, T. Wiegert, G. Homuth, and W. Schumann. 2001. Development of a new integration site within the Bacillus subtilis chromosome and construction of compatible expression cassettes. J. Bacteriol. 183: 2696-2699.
20. Harwood, C. R., and S. M. Cutting (ed.). 1990. Molecular methods for Bacillus. John Wiley & Sons, Chichester, United Kingdom.
21. Horinouchi, S., and B. Weisblum. 1982. Nucleotide sequence and functional map of pE194, a plasmid that specifies inducible resistance to macrolide, lincosamide, and streptogramin type B antibiotics. J. Bacteriol. 150:804-814.
22. Kasahara, Y., S. Nakai, N. Ogasawara, K. Yata, and Y. Sadaie. 1997. Sequence analysis of the groESL-cotA region of the Bacillus subtilis genome, containing the restriction/modification system genes. DNA Res. 4:335-339.
23. Kobayashi, K., S. D. Ehrlich, A. Albertini, G. Amati, K. K. Andersen, M. Arnaud, K. Asai, S. Ashikaga, S. Aymerich, P. Bessieres, F. Boland, S. C. Brignell, S. Bron, K. Bunai, J. Chapuis, L. C. Christiansen, A. Danchin, M. Debarbouille, E. Dervyn, E. Deuerling, K. Devine, S. K. Devine, O. Dreesen, J. Errington, S. Fillinger, S. J. Foster, Y. Fujita, A. Galizzi, R. Gardan, C. Eschevins, T. Fukushima, K. Haga, C. R. Harwood, M. Hecker, D. Hosoya, M. F. Hullo, H. Kakeshita, D. Karamata, Y. Kasahara, F. Kawamura, K. Koga, P. Koski, R. Kuwana, D. Imamura, M. Ishimaru, S. Ishikawa, I. Ishio, D. Le Coq, A. Masson, C. Mauel, R. Meima, R. P. Mellado, A. Moir, S. Moriya, E. Nagakawa, H. Nanamiya, S. Nakai, P. Nygaard, M. Ogura, T. Ohanan, M. O'Reilly, M. O'Rourke, Z. Pragai, H. M. Pooley, G. Rapoport, J. P. Rawlins, L. A. Rivas, C. Rivolta, A. Sadaie, Y. Sadaie, M. Sarvas, T. Sato, H. H. Saxild, E. Scanlan, W. Schumann, J. F. Seegers, J. Sekiguchi, A. Sekowska, S. J. Seror, M. Simon, P. Stragier, R. Studer, H. Takamatsu, T. Tanaka, M. Takeuchi, H. B. Thomaides, V. Vagner, J. M. van Dijl, K. Watabe, A. Wipat, H. Yamamoto, M. Yamamoto, Y. Yamamoto, K. Yamane, K. Yata, K. Yoshida, H. Yoshikawa, U. Zuber, and N. Ogasawara. 2003. Essential Bacillus subtilis genes. Proc. Natl. Acad. Sci. USA 100:4678-4683.
24. Kuhn, R., and R. M. Torres. 2002. Cre/loxP recombination system and gene targeting. Methods Mol. Biol. 180:175-204.
25. Kunst, F., N. Ogasawara, I. Moszer, A. M. Albertini, G. Alloni, V. Azevedo, M. G. Bertero, P. Bessieres, A. Bolotin, S. Borchert, R. Borriss, L. Boursier, A. Brans, M. Braun, S. C. Brignell, S. Bron, S. Brouillet, C. V. Bruschi, B. Caldwell, V. Capuano, N. M. Carter, S. K. Choi, J. J. Codani, I. F. Connerton, N. J. Cummings, R. A. Daniel, F. Denizot, K. M. Devine, A. Dusterhoft, S. D. Ehrlich, P. T. Emmerson, K. D. Entian, J. Errington, C. Fabret, E. Ferrari, D. Foulger, C. Fritz, M. Fujita, Y. Fujita, S. Fuma, A. Galizzi, N. Galleron, S. Y. Ghim, P. Glaser, A. Goffeau, E. J. Golightly, G. Grandi, G. Guiseppi, B. J. Guy, K. Haga, J. Haiech, C. R. Harwood, A. Henaut, H. Hilbert, S. Holsappel, S. Hosono, M. F. Hullo, M. Itaya, L. Jones, B. Joris, D. Karamata, Y. Kasahara, M. Klaerr Blanchard, C. Klein, Y. Kobayashi, P. Koetter, G. Koningstein, S. Krogh, M. Kumano, K. Kurita, A. Lapidus, S. Lardinois, J. Lauer, V. Lazarevic, S. M. Lee, A. Levine, H. Liu, S. Masuda, C. Mauel, C. Medigue, N. Medina, R. P. Mellado, M. Mizuno, D. Moestl, S. Nakai, M. Noback, D. Noone, M. O'Reilly, K. Ogawa, A. Ogiwara, B. Oudega, S. H. Park, V. Parro, T. M. Pohl, D. Portetelle, S. Porwollik, A. M. Prescott, E. Presecan, P. Pujic, B. Purnelle, G. Rapoport, M. Rey, S. Reynolds, M. Rieger, C. Rivolta, E. Rocha, B. Roche, M. Rose, Y. Sadaie, T. Sato, E. Scanlan, S. Schleich, R. Schroeter, F. Scoffone, J. Sekiguchi, A. Sekowska, S. J. Seror, P. Serror, B. S. Shin, B. Soldo, A. Sorokin, E. Tacconi, T. Takagi, H. Takahashi, K. Takemaru, M. Takeuchi, A. Tamakoshi, T. Tanaka, P. Terpstra, A. Tognoni, V. Tosato, S. Uchiyama, M. Vandenbol, F. Vannier, A. Vassarotti, A. Viari, R. Wambutt, E. Wedler, H. Wedler, T. Weitzenegger, P. Winters, A. Wipat, H. Yamamoto, K. Yamane, K. Yasumoto, K. Yata, K. Yoshida, H. F. Yoshikawa, E. Zumstein, H. Yoshikawa, and A. Danchin. 1997. The complete genome sequence of the gram-positive bacterium Bacillus subtilis. Nature 390:249-256.
26. Lambert, J. M., R. S. Bongers, and M. Kleerebezem. 2007. Cre-lox-based system for multiple gene deletions and selectable-marker removal in Lactobacillus plantarum. Appl. Environ. Microbiol. 73:1126-1135.
27. Mascher, T., N. G. Margulis, T. Wang, R. W. Ye, and J. D. Helmann. 2003. Cell wall stress responses in Bacillus subtilis: the regulatory network of the bacitracin stimulon. Mol. Microbiol. 50:1591-1604.
28. Micka, B., N. Groch, U. Heinemann, and M. A. Marahiel. 1991. Molecular cloning, nucleotide sequence and characterization of the Bacillus subtilis gene encoding the DNA-binding protein HBsu. J. Bacteriol. 173:3191-3198.
29. Oliver, S. G., M. K. Winson, D. B. Kell, and F. Baganz. 1998. Systematic functional analysis of the yeast genome. Trends Biotechnol 16:373-378.
30. Sambrook, J., E. F. Fritsch, and T. Maniatis. 1989. Molecular cloning: a laboratory manual, 2nd ed. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.
31. Schallmey, M., A. Singh, and O. P. Ward. 2004. Developments in the use of Bacillus species for industrial production. Can. J. Microbiol. 50:1-17.
32. Shevchuk, N. A., A. V. Bryksin, Y. A. Nusinovich, F. C. Cabello, M. Sutherland, and S. Ladisch. 2004. Construction of long DNA molecules using long PCR-based fusion of several fragments simultaneously. Nucleic Acids Res. 32:e19.
33. Stragier, P., C. Bonamy, and C. Karmazyn-Campelli. 1988. Processing of a sporulation sigma factor in Bacillus subtilis: how morphological structure could control gene expression. Cell 52:697-704.
34. Suzuki, N., H. Nonaka, Y. Tsuge, M. Inui, and H. Yukawa. 2005. New multiple-deletion method for the Corynebacterium glutamicum genome, using a mutant lox sequence. Appl. Environ. Microbiol. 71:8472-8480.
35. Wach, A. 1996. PCR-synthesis of marker cassettes with long flanking homology regions for gene disruptions in S. cerevisiae. Yeast 12:259-265.
36. Westers, H., R. Dorenbos, J. M. van Dijl, J. Kabel, T. Flanagan, K. M. Devine, F. Jude, S. J. Séror, A. C. Beekman, E. Darmon, C. Eschevins, A. de Jong, S. Bron, O. P. Kuipers, A. M. Albertini, H. Antelmann, M. Hecker, N. Zamboni, U. Sauer, C. Bruand, D. S. Ehrlich, J. C. Alonso, M. Salas, and W. J. Quax. 2003. Genome engineering reveals large dispensable regions in Bacillus subtilis. Mol. Biol. Evol. 20:2076-2090.
37. Yanisch-Perron, C., J. Vieira, and J. Messing. 1985. Improved m13 phage cloning vectors and host strains: nucleotide sequences of the m13mp18 and pUC19 vectors. Gene 33:103-119.
38. Zhang, X. Z., X. Yan, Z. L. Cui, Q. Hong, and S. P. Li. 2006. mazF, a novel counter-selectable marker for unmarked chromosomal manipulation in Bacillus subtilis. Nucleic Acids Res. 34:e71.
39. Zhang, X. Z., Z. L. Cui, Q. Hong, and S. P. Li. 2005. High-level expression and secretion of methyl parathion hydrolase in Bacillus subtilis WB800. Appl. Environ. Microbiol. 71:4101-4103.
40. Zhangli, C., L. Shunpeng, and F. Guoping. 2001. Isolation of methyl parathion-degrading strain M6 and cloning of the methyl parathion hydrolase gene. Appl. Environ. Microbiol. 67:4922-4925.