Cre-lox-based method for generation of large deletions within the genomic magnetosome island of magnetospirillum gryphiswaldense

Applied and Environmental Microbiology

Volumn 76, Issue 8, 2010, Pages 2439-2444

  Ullrich, Susanne ^a   Schüler, Dirk ^a  

^a UNIVERSITY OF MUNICH   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

CRE RECOMBINASE; CROSSOVER EVENTS; DELETION METHODS; GENE FUNCTION; GENETIC ANALYSIS; GENOME ENGINEERING; GENOMIC FRAGMENTS; HOMOLOGOUS RECOMBINATION; MAGNETOSPIRILLUM GRYPHISWALDENSE; MAGNETOTACTIC BACTERIA; NORMAL GROWTH; TARGET REGIONS;

BACTERIOLOGY; BIOMINERALIZATION; RADIO INTERFERENCE;

GENES;

BACTERIAL DNA; RECOMBINASE;

BACTERIUM; BIOMINERALIZATION; CHROMOSOME; GENE EXPRESSION; GENETIC ANALYSIS; GENETIC ENGINEERING; GENOME; GENOMICS; PLASMID; RECOMBINATION;

ARTICLE; GENE DELETION; GENE EXPRESSION REGULATION; GENETIC RECOMBINATION; GENETICS; GENOMIC ISLAND; MAGNETOSOME; MAGNETOSPIRILLUM; METABOLISM; METHODOLOGY; MICROBIAL GENETICS; PLASMID;

DNA, BACTERIAL; GENETICS, MICROBIAL; GENOMIC ISLANDS; MAGNETOSOMES; MAGNETOSPIRILLUM; MUTAGENESIS, INSERTIONAL; PLASMIDS; RECOMBINASES; RECOMBINATION, GENETIC; SEQUENCE DELETION;

BACTERIA (MICROORGANISMS); MAGNETOSPIRILLUM; MAGNETOSPIRILLUM GRYPHISWALDENSE;

EID: 77950591971     PISSN: 00992240     EISSN: 10985336     Source Type: Journal    
DOI: 10.1128/AEM.02805-09     Document Type: Article

References (49)

1. Ayres, E. K., V. J. Thomson, G. Merino, D. Balderes, and D. H. Figurski. 1993. Precise deletions in large bacterial genomes by vector-mediated excision (VEX). The trfA gene of promiscuous plasmid RK2 is essential for replication in several gram-negative hosts. J. Mol. Biol. 230: 174-185.
2. Bazylinski, D. A., and R. B. Frankel. 2004. Magnetosome formation in prokaryotes. Nat. Rev. Microbiol. 2: 217-230.
3. 3. Bertani, G. 2004. Lysogeny at mid-twentieth century: Pl, P2, and other experimental systems. J. Bacteriol. 186: 595-600. (Pubitemid 38129635)
4. Bucholtz, F. 2008. Principles of site-specific recombinase (SSR) technology. J. Vis. Exp. pii: 718.
5. Faivre, D., and D. Schüler. 2008. Magnetotactic bacteria and magnetosomes. Chem. Rev. 108: 4875-4898.
6. Ghosh, K., and G. D. Van Duyne. 2002. Cte-loxP biochemistry. Methods 28: 374-383.
7. Gopaul, D. N., F. Guo, and G. D. Van Duyne. 1998. Structure of the Holliday junction intermediate in Cie-loxP site-specific recombination. EMBO J. 17: 4175-4187.
8. Grünberg, K, E. C. Müller, A. Otto, R. Reszka, D. Linder, M. Kube, R. Reinhardt, and D. Schüler. 2004. Biochemical and proteomic analysis of the magnetosome membrane in Magnetospirillum gryphiswaldense. Appl. Environ. Microbiol. 70: 1040-1050.
9. Grünberg, K., C. Wawer, B. M. Tebo, and D. Schüler. 2001. A large gene cluster encoding several magnetosome proteins is conseived in different species of magnetotactic bacteria. Appl. Environ. Microbiol. 67: 4573-4582.
10. Heyen, U., and D. Schüler. 2003. Growth and magnetosome formation by microaerophilic Magnetospirillum strains in an oxygen-controlled fermentor. Appl. Microbiol. Biotechnol. 61: 536-544.
11. Huang, Y., W. Zhang, W. Jiang, C. Rong, and Y. Li. 2007. Disruption of a fur-like gene inhibits magnetosome formation in Magnetospirillum gryphiswaldense MSR-1. Biochemistry (Moscow) 72: 1247-1253.
12. Jogler, C, M. Kube, S. Schübbe, S. Ullrich, H. Teeling, D. A. Bazylinski, R. Reinhardt, and D. Schüler. 2009. Comparative analysis of magnetosome gene clusters in magnetotactic bacteria provides further evidence for horizontal gene transfer. Environ. Microbiol. 11: 1267-1277.
13. Jogler, C, W. Lin, A. Meyerdierks, M. Kube, E. Katzmann, C. Flies, Y. Pan, R. Amann, R. Reinhardt, and D. Schüler. 2009. Towards cloning the magnetotactic metagenome: identification of magnetosome island gene clusters in uncultivated magnetotactic bacteria from different aquatic sediments. Appl. Environ. Microbiol. 75: 3972-3979.
14. Jogler, C, and D. Schüler. 2006. Genetic analysis of magnetosome biomineralization. In D. Schüler (ed.), Magnetoreception and magnetosomes in bacteria. Springer, Heidelberg, Germany.
15. Jogler, C, and D. Schüler. 2009. Genomics, genetics, and cell biology of magnetosome formation. Annu. Rev. Microbiol. 63: 501-521.
16. 16.Katzen,F.,A.Becker,M.V.Ielmini,C.G.Oddo,andL.IeIpL1999. Newmobilizablevectorssuitableforgenereplacementingram- negativebacteriaandtheiruseinmappingofthe3'endoftheXanthomonascampestrispv. campestrisgumOperon.Appl.Environ.Microbiol.65:278-282.(Pubitemid29029649)
17. Kim, T. Y., H. U. Kim, J. M. Park, H. Song, J. S. Kim, and S. Y. Lee. 2007. Genome-scale analysis of Mannheimia succiniciproducens metabolism. Biotechnol. Bioeng. 97: 657-671.
18. 18. Komeili, A., Z. Li, D. K. Newman, and G. J. Jensen. 2006. Magnetosomes are cell membrane invaginations organized by the actin-like protein MamK. Science 311: 242-245. (Pubitemid 43108192)
19. Komeili, A., H. Vali, T. J. Beveridge, and D. Newman. 2004. Magnetosome vesicles are present prior to magnetite formation and MamA is required for their activation. Proc. Nat. Acad. Sci. U. S. A. 101: 3839-3844.
20. Kovach, M. E., R. W. Phillips, P. H. Elzer, R. M. Roop Π, and K. M. Peterson. 1994. pBBRlMCS: a broad-host-range cloning vector. Biotechniques 16: 800-802.
21. Kuhn, R., and R. M. Torres. 2002. Cre/loxP recombination system and gene targeting. Methods Mol. Biol. 180: 175-204.
22. 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.
23. Leiblg, M., B. Krismer, M. Kolb, A. Friede, F. Gotz, and R. Bertram. 2008. Marker removal in staphylococci via Cre recombinase and different lox sites. Appl. Environ. Microbiol. 74: 1316-1323.
24. Marmur, J. 1961. A procedure for the isolation of deoxiribonucleic acid from microorganisms. J. Mol. Biol. 3: 208-218.
25. Marx, C. J., and M. E. Lidstrom. 2002. Broad-host-range Cre-lox system for antibiotic marker recycling in gram-negative bacteria. Biotechniques 33: 1062-1067.
26. Matsunaga, T., M. Nemoto, A. Arakaki, and M. Tanaka. 2009. Proteomic analysis of irregular, bullet-shaped magnetosomes in the sulphate-reducing magnetotactic bacteriumDesulfovibrio magneticus RS-1. Proteomics 9: 3341-3352.
27. Matsunaga, T., Y. Okamura, Y. Fukuda, A. T. Wahyudi, Y. Murase, and H. Takeyama. 2005. Complete genome sequence of the facultative anaerobic magnetotactic bacterium Magnetospirillum sp. strain AMB-1. DNA Res. 12: 157-166.
28. Nakamura, C, J. G. Burgess, K. Sode, and T. Matsunaga. 1995. An ironregulated gene, magA, encoding an iron transport protein of Magnetospirillum sp. strain AMB-1. J. Biol. Chem. 270: 28392-28396.
29. 29. Richter, M., M. Kube, D. A. Bazylinski, T. Lombardot, F. O. Glöckner, R. Reinhardt, and D. Schüler. 2007. Comparative genome analysis of four magnetotactic bacteria reveals a complex set of group-specific genes implicated in magnetosome biomineralization and function. J. Bacteriol. 189: 4899-4910. (Pubitemid 47025602)
30. Sambrook, J., and D. W. Russell. 2001. Molecular cloning: a laboratory manual, 3rd ed. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
31. Scheffel, A., A. Gärdes, K. Grünberg, G. Wanner, and D. Schüler. 2008. The major magnetosome proteins MamGFDC are not essential for magnetite biomineralization in Magnetospirillum gryphiswaldense but regulate the size of magnetosome crystals. J. Bacteriol. 190: 377-386.
32. 32. Scheffel, A., M. Gruska, D. Faivre, P. Graumann, A. Linaroudis, J. M. Plitzko, and D. Schüler. 2006. An acidic protein aligns magnetosomes along a filamentous structure in magnetotactic bacteria. Nature 440: 110-115. (Pubitemid 43336277)
33. Scheffel, A., and D. Schüler. 2007. The acidic repetitive domain of the Magnetospirillum gryphiswaldense MamJ protein displays hypervariability but is not required for magnetosome chain assembly. J. Bacteriol. 189: 6437-6446.
34. Schübbe, S., M. Kube, A. Scheffel, C. Wawer, U. Heyen, A. Meyerdierks, M. H. Madkour, F. Mayer, R. Reinhardt, and D. Schüler. 2003. Characterization of a spontaneous nonmagnetic mutant of Magnetospirillum gryphiswaldense reveals a large deletion comprising a putative magnetosome island. J. Bacteriol. 185: 5779-5790.
35. Schübbe, S., T. J. Williams, G. Xie, H. E. Kiss, T. S. Brettin, D. Martinez, C. A. Ross, D. Schüler, B. L. Cox, K. H. Nealson, and D. A. Bazylinski. 2009. Complete genome sequence of the chemolithoautotrophic marine magnetotactic coccus strain MC-1. Appl. Environ. Microbiol. 75: 4835-4852.
36. Schübbe, S., C. Würdemann, J. Peplies, U. Heyen, C. Wawer, F. O. Glöckner, and D. Schüler. 2006. Transcriptional organization and regulation of magnetosome operons in Magnetospirillum gryphiswaldense. Appl. Environ. Microbiol. 72: 5757-5765.
37. Schüler, D. 2008. Genetics and cell biology of magnetosome formation in magnetotactic bacteria. FEMS Microbiol. Rev. 32: 654-672.
38. Schüler, D., R. Uhl, and E. Baeuerlein. 1995. A simple light-scattering method to assay magnetism in Magnetospirillum gryphiswaldense. FEMS Microbiol. Lett. 132: 139-145.
39. Schultheiss, D., R. Handrick, D. Jendrossek, M. Hanzlik, and D. Schüler. 2005. The presumptive magnetosome protein Mmsl6 is a PHB-granule bound protein (phasin) in Magnetospirillum gryphiswaldense. J. Bacteriol. 187: 2416-2425.
40. Schultheiss, D., M. Kube, and D. Schüler. 2004. Inactivation of the fiagellin gene flaA in Magnetospirillum gryphiswaldense results in non-magnetotactic mutants lacking flagellar filaments. Appl. Environ. Microbiol. 70: 3624-3631.
41. Schultheiss, D., and D. Schüler. 2003. Development of a genetic system for Magnetospirillum gryphiswaldense. Arch. Microbiol. 179: 89-94.
42. Sternberg, N., and D. Hamilton. 1981. Bacteriophage Pl site-specific recombination. I. Recombination between loxP sites. J. MoL Biol. 150: 467-486.
43. 43. Suzuki, N., H. Nonaka, Y. Tsuge, M. Inui, and H. Yukawa. 2005. New multiple-deletion method for the Corynebacterium glutamicum genome, using a mutant lax sequence. Appl. Environ. Microbiol. 71: 8472-8480. (Pubitemid 41803978)
44. Suzuki, N., H. Nonaka, Y. Tsuge, S. Okayama, L Masayuki, and H. Yukawa. 2005. Multiple large segment deletion method for Corynebacterium glutamicum. Appl. Microbiol. Biotechnol. 69: 151-161.
45. 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.
46. 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.
47. Ullrich, S., M. Kube, S. Schübbe, R. Reinhardt, and D. Schüler. 2005. A hypervariable 130-kilobase genomic region of Magnetospirillum gryphiswaldense comprises a magnetosome island which undergoes frequent rearrangements during stationary growth. J. Bacteriol. 187: 7176-7184.
48. Van Duyne, G. D. 2001. A structural view of Cre-loxP site-specific recombination. Annu. Rev. Biophys. Biomol. Struct. 30: 87-104.
49. Yan, X., H. J. Yu, Q. Hong, and S. P. Li. 2008. Cre/lox system and PCR based genome engineering in Bacillus subtilis. Appl. Environ. Microbiol. 74: 5556-5562.