New multiple-deletion method for the Corynebacterium glutamicum genome, using a mutant lox sequence

Applied and Environmental Microbiology

Volumn 71, Issue 12, 2005, Pages 8472-8480

  Suzuki, Nobuaki ^a   Nonaka, Hiroshi ^a   Tsuge, Yota ^a,b   Inui, Masayuki ^a   Yukawa, Hideaki ^a,b  

^a RESEARCH INSTITUTE OF INNOVATIVE TECHNOLOGY FOR THE EARTH   (Japan)

^b NARA INSTITUTE OF SCIENCE AND TECHNOLOGY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

GENETIC ENGINEERING; MICROBIOLOGY; MICROORGANISMS;

MULTIPLE-DELETION METHOD; MUTANT LOX SITE; OPEN READING FORM;

GENES;

DETECTION METHOD; MOLECULAR ANALYSIS;

ANALYTIC METHOD; ARTICLE; BACTERIAL GENE; BACTERIAL GROWTH; CONTROLLED STUDY; CORYNEBACTERIUM GLUTAMICUM; GENE DELETION; GENE FUNCTION; GENE MUTATION; GENE REARRANGEMENT; GENE TARGETING; GENETIC ANALYSIS; LOX GENE; NONHUMAN; NUCLEOTIDE SEQUENCE; OPEN READING FRAME; PREDICTION; SEQUENCE ANALYSIS; TECHNIQUE;

BASE SEQUENCE; CORYNEBACTERIUM GLUTAMICUM; DNA PRIMERS; DNA, BACTERIAL; GENE DELETION; GENES, BACTERIAL; GENOME, BACTERIAL; PLASMIDS; RECOMBINATION, GENETIC; RESTRICTION MAPPING;

BACTERIA (MICROORGANISMS); CORYNEBACTERIUM GLUTAMICUM;

EID: 29144438996     PISSN: 00992240     EISSN: None     Source Type: Journal    
DOI: 10.1128/AEM.71.12.8472-8480.2005     Document Type: Article

References (39)

1. 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.
2. Araki, K., M. Araki, and K. Yamamura. 1997. Targeted integration of DNA using mutant lox sites in embryonic stem cells. Nucleic Acids Res. 25:868-872.
3. Campo, N., M. L. Daveran-Mingot, K. Leenhouts, P. Ritzenthaler, and P. Le Bourgeois. 2002. Cre-loxP recombination system for large genome rearrangements in Lactococcus lactis. Appl. Environ. Microbiol. 68:2359-2367.
4. Casjens, S. 2003. Prophages and bacterial genomics: what have we learned so far? Mol. Microbiol. 49:277-300.
5. Eikmanns, B. J., E. Kleinertz, W. Liebl, and H. Sahm. 1991. A family of Corynebacterium glutamicum/Escherichia coli shuttle vectors for cloning, controlled gene expression, and promoter probing. Gene 102:93-98.
6. Fukiya, S., H. Mizoguchi, and H. Mori. 2004. An improved method for deleting large regions of Escherichia coli K-12 chromosome using a combination of Cre/loxP and lambda Red. FEMS Microbiol. Lett. 234:325-331.
7. Garbe, T. R., N. Suzuki, M. Inui, and H. Yukawa. 2004. Inhibitor-associated transposition events in Corynebacterium glutamicum. Mol. Genet. Genomics 271:729-741.
8. Giaever, G., A. M. Chu, L. Ni, C. Connelly, L. Riles, S. Veronneau, S. Dow, A. Lucau-Danila, K. Anderson, B. Andre, A. P. Arkin, A. Astromoff, M. El-Bakkoury, R. Bangham, R. Benito, S. Brachat, S. Campanaro, M. Curtiss, K. Davis, A. Deutschbauer, K. D. Entian, P. Flaherty, F. Foury, D. J. Garfinkel, M. Gerstein, D. Gotte, U. Guldener, J. H. Hegemann, S. Hempel, Z. Herman, D. F. Jaramillo, D. E. Kelly, S. L. Kelly, P. Kotter, D. LaBonte, D. C. Lamb, N. Lan, H. Liang, H. Liao, L. Liu, C. Luo, M. Lussier, R. Mao, P. Menard, S. L. Ooi, J. L. Revuella, C. J. Roberts, M. Rose, P. Ross-Macdonald, B. Scherens, G. Schimmack, B. Shafer, D. D. Shoemaker, S. Sookhai-Mahadeo, R. K. Storms, J. N. Strathern, G. Valle, M. Voet, G. Volckaert, C. Y. Wang, T. R. Ward, J. Wilhelmy, E. A. Winzeler, Y. Yang, G. Yen, E. Youngman, K. Yu, H. Bussey, J. D. Boeke, M. Snyder, P. Philippsen, R. W. Davis, and M. Johnston. 2002. Functional profiling of the Saccharomyces cerevisiae genome. Nature 418:387-391.
9. Gopaul, D. N., F. Guo, and G. D. Van Duyne. 1998. Structure of the Holliday junction intermediate in Cre-loxP site-specific recombination. EMBO J. 17:4175-4187.
10. Goryshin, I. Y., T. A. Naumann, J. Apodaca, and W. S. Reznikoff. 2003. Chromosomal deletion formation system based on Tn5 double transposition: use for making minimal genomes and essential gene analysis. Genome Res. 13:644-653.
11. Hacker, J., G. Blum-Oehler, I. Muhldorfer, and H. Tschape. 1997. Pathogenicity islands of virulent bacteria: structure, function and impact on microbial evolution. Mol. Microbiol. 23:1089-1097.
12. Hashimoto, M., T. Ichimura, H. Mizoguchi, K. Tanaka, K. Fujimitsu, K. Keyamura, T. Ote, T. Yamakawa, Y. Yamazaki, H. Mori, T. Katayama, and J. Kato. 2005. Cell size and nucleoid organization of engineered Escherichia coli cells with a reduced genome. Mol. Microbiol. 55:137-149.
13. Hoess, R. H., M. Ziese, and N. Sternberg. 1982. Pl site-specific recombination: nucleotide sequence of the recombining sites. Proc. Natl. Acad. Sci. USA 79:3398-3402.
14. Ikeda, M., and S. Nakagawa. 2003. The Corynebacterium glutamicum genome: features and impacts on biotechnological processes. Appl. Microbiol. Biotechnol. 62:99-109.
15. Inui, M., S. Murakami, S. Okino, H. Kawaguchi, A. A. Vertès, and H. Yukawa. 2004. Metabolic analysis of Corynebacterium glutamicum during lactate and succinate productions under oxygen deprivation conditions. J. Mol. Microbiol. Biotechnol. 7:182-196.
16. Inui, M., Y. Tsuge, N. Suzuki, A. A. Vertès, and H. Yukawa. 2005. Isolation and characterization of a native composite transposon, Tn14751, carrying 17.4 kilobases of Corynebacterium glutamicum chromosomal DNA. Appl. Environ. Microbiol. 71:407-416.
17. Kalinowski, J., B. Bathe, D. Bartels, N. Bischoff, M. Bott, A. Burkovski, N. Dusch, L. Eggeling, B. J. Eikmanns, L. Gaigalat, A. Goesmann, M. Hartmann, K. Huthmacher, R. Krämer, B. Linke, A. C. McHardy, F. Meyer, B. Möckel, W. Pfefferle, A. Pühler, D. A. Rey, C. Rückert, O. Rupp, H. Sahm, V. F. Wendisch, I. Wiegräbe, and A. Tauch. 2003. The complete Corynebacterium glutamicum ATCC 13032 genome sequence and its impact on the production of L-aspartate-derived amino acids and vitamins. J. Biotechnol. 104:5-25.
18. Kinoshita, S. 1985. Glutamic acid bacteria, p. 115-146. In A. L. Demain and N. A. Solomon (ed.), Biology of industrial microorganisms. Cummings, London, United Kingdom.
19. 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.
20. Kolisnychenko, V., G. Plunkett III, C. D. Herring, T. Feher, J. Posfai, F. R. Blattner, and G. Posfai. 2002. Engineering a reduced Escherichia coli genome. Genome Res. 12:640-647.
21. Kuhn, R., and R. M. Torres. 2002. Cre/loxP recombination system and gene targeting. Methods Mol. Biol. 180:175-204.
22. Lee, L., and P. D. Sadowski. 2001. Directional resolution of synthetic Holliday structures by the Cre recombinase. J. Biol. Chem. 276:31092-31098.
23. Malumbres, M., L. M. Mateos, and J. F. Martin. 1995. Microorganisms for amino acid production: Escherichia coli and corynebacteria, p. 423-469. In Y. H. Hui and G. G. Kachatourians (ed.), Food biotechnology microorganisms, vol. 2. VCH Publishers, New York, N.Y.
24. McClelland, M., L. Florea, K. Sanderson, S. W. Clifton, J. Parkhill, C. Churcher, G. Dougan, R. K. Wilson, and W. Miller. 2000. Comparison of the Eseherichia coli K-12 genome with sampled genomes of a Klebsiella pneumoniae and three Salmonella enterica serovars, Typhimurium, Typhi and Paratyphi. Nucleic Acids Res. 28:4974-4986.
25. Mira, A., H. Ochman, and N. A. Moran. 2001. Deletional bias and the evolution of bacterial genomes. Trends Genet. 17:589-596.
26. Mori, H., K. Isono, T. Horiuchi, and T. Miki. 2000. Functional genomics of Escherichia coli in Japan. Res. Microbiol. 151:121-128.
27. Ochman, H., and I. B. Jones. 2000. Evolutionary dynamics of full genome content in Escherichia coli. EMBO J. 19:6637-6643.
28. Ohnishi, J, M. Hayashi, S. Mitsuhashi, and M. Ikeda. 2003. Efficient 40°C fermentation of L-lysine by a new Corynebacterium glutamicum mutant developed by genome breeding. Appl. Microbiol. Biotechnol. 62:69-75.
29. Qin, M., C. Bayley, T. Stockton, and D. W. Ow. 1994. Cre recombinase-mediated site-specific recombination between plant chromosomes. Proc. Natl. Acad. Sci. USA 91:1706-1710.
30. Riley, M., and M. H. Serres. 2000. Interim report on genomics of Escherichia coli. Annu. Rev. Microbiol. 54:341-411.
31. 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.
32. Suzuki, N., Y. Tsuge, M. Inui, and H. Yukawa. 2005. Cre/loxP-mediated deletion system for large genome rearrangements in Corynebacterium glutamicum. Appl. Microbiol. Biotechnol. 67:225-233.
33. Suzuki, N., H. Nonaka, Y. Tsuge, S. Okayama, M. Inui, and H. Yukawa. Multiple large segment deletion method for Corynebacterium glutamicum. Appl. Microbiol. Biotechnol., in press.
34. Suzuki, N., S. Okayama, H. Nonaka, Y. Tsuge, M. Inui, and H. Yukawa. 2005. Large-scale engineering of the Corynebacterium glutamicum genome. Appl. Environ. Microbiol. 71:3369-3372.
35. Tsuge, Y., K. Ninomiya, N. Suzuki, M. Inui, and H. Yukawa. 2005. A new insertion sequence, IS14999, from Corynebacterium glutamicum. Microbiology 151:501-508.
36. Van Deursen, J., M. Fornerod, B. Van Rees, and G. Grosveld. 1995. Cre-mediated site-specific translocation between nonhomologous mouse chromosomes. Proc. Natl. Acad. Sci. USA 92:7376-7380.
37. Vertès, A. A., M. Inui, M. Kobayashi, Y. Kurusu, and H. Yukawa. 1993. Presence of mrr- and mcr-like restriction systems in coryneform bacteria. Res. Microbiol. 144:181-185.
38. Vertès, A. A., M. Inui, M. Kobayashi, Y. Kurusu, and H. Yukawa. 1994. Isolation and characterization of IS31831, a transposable element from Corynebacterium glutamicum. Mol. Microbiol. 11:739-746.
39. Yu, B. J., B. H. Sung, M. D. Koob, C. H. Lee, J. H. Lee, W. S. Lee, M. S. Kim, and S. C. Kim. 2002. Minimization of the Escherichia coli genome using a Tn5-targeted Cre/loxP excision system. Nat. Biotechnol. 20:1018-1023.