A hypervariable 130-kilobase genomic region of Magnetospirillum gryphiswaldense comprises a magnetosome island which undergoes frequent rearrangements during stationary growth

Journal of Bacteriology

Volumn 187, Issue 21, 2005, Pages 7176-7184

  Ullrich, Susanne ^a   Kube, Michael ^b   Schübbe, Sabrina ^a   Reinhardt, Richard ^b   Schüler, Dirk ^a  

^a MAX PLANCK INSTITUTE FOR MARINE MICROBIOLOGY   (Germany)

^b MAX PLANCK INSTITUTE FOR MOLECULAR GENETICS   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

DNA;

ANIMAL CELL; ARTICLE; BIOMINERALIZATION; GENE DELETION; GENE IDENTIFICATION; GENE INSERTION; GENE REARRANGEMENT; GENETIC POLYMORPHISM; GENETIC VARIABILITY; MAGNETOSOME ISLAND; MAGNETOSPIRILLUM; MAGNETOSPIRILLUM GRYPHISWALDENSE; MOLECULAR CLONING; NONHUMAN; NUCLEOTIDE SEQUENCE; OXIDATIVE STRESS; PHENOTYPE; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; PSEUDOGENE; SOUTHERN BLOTTING;

BLOTTING, SOUTHERN; CYTOPLASMIC VESICLES; DNA TRANSPOSABLE ELEMENTS; DNA, BACTERIAL; FERROSOFERRIC OXIDE; GENE DELETION; GENE REARRANGEMENT; GENES, BACTERIAL; GENOME, BACTERIAL; GENOMIC ISLANDS; MAGNETICS; MAGNETOSPIRILLUM; MOLECULAR SEQUENCE DATA; MUTATION; POLYMERASE CHAIN REACTION; POLYMORPHISM, GENETIC; PSEUDOGENES; SEQUENCE ANALYSIS, DNA; SEQUENCE HOMOLOGY;

ANIMALIA; BACTERIA (MICROORGANISMS); MAGNETOSPIRILLUM; MAGNETOSPIRILLUM GRYPHISWALDENSE;

EID: 27144485750     PISSN: 00219193     EISSN: None     Source Type: Journal    
DOI: 10.1128/JB.187.21.7176-7184.2005     Document Type: Article

References (45)

1. Albertini, A. M., M. Hofer, M. P. Calos, and J. H. Miller. 1982. On the formation of spontaneous deletions: the importance of short sequence homologies in the generation of large deletions. Cell 29:319-328.
2. Altschul, S. F., T. L. Madden, A. A. Schaffer, J. Zhang, Z. Zhang, W. Miller, and D. J. Lipman. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25:3389-3402.
3. Apweiler, R., T. K. Attwood, A. Bairoch, A. Bateman, E. Birney, M. Biswas, P. Bucher, L. Cerutti, F. Corpet, M. D. Croning, R. Durbin, L. Falquet, W. Fleischmann, J. Gouzy, H. Hermjakob, N. Hulo, I. Jonassen, D. Kahn, A. Kanapin, Y. Karavidopoulou, R. Lopez, B. Marx, N. J. Mulder, T. M. Oinn, M. Pagni, and F. Servant. 2001. The InterPro database, an integrated documentation resource for protein families, domains and functional sites. Nucleic Acids Res. 29:37-40.
4. Bach, S., C. Buchrieser, M. Prentice, A. Guiyoule, T. Msadek, and E. Carniel. 1999. The high-pathogenicity island of Yersinia enterocolitica Ye8081 undergoes low-frequency deletion but not precise excision, suggesting recent stabilization in the genome. Infect. Immun. 67:5091-5099.
5. Baxevanis, A. D. 2003. The Molecular Biology Database Collection: 2003 update. Nucleic Acids Res. 31:1-12.
6. Bazylinski, D. A., and R. B. Frankel. 2004. Magnetosome formation in prokaryotes. Nat. Rev. Microbiol. 2:217-230.
7. leuX. J. Bacteriol. 187:2469-2482.
8. Blakemore, R., D. Maratea, and R. S. Wolfe. 1979. Isolation and pure culture of a freshwater magnetic spirillum in chemically defined medium. J. Bacteriol. 140:720-729.
9. Chien, M. C., I. Morozova, S. Shi, H. Sheng, J. Chen, S. M. Gomez, G. Asamani, K. Hill, J. Nuara, M. Feder, J. Rineer, J. J. Greenberg, V. Steshenko, S. H. Park, B. Zhao, E. Teplitskaya, J. R. Edwards, S. Pampou, A. Georghiou, I. C. Chou, W. Iannuccilli, M. E. Ulz, D. H. Kim, A. Geringer-Sameth, C. Goldsberry, P. Morozov, S. G. Fischer, G. Segal, X. Qu, A. Rzhetsky, P. Zhang, E. Cayanis, P. J. De Jong, J. Ju, S. Kalachikov, H. A. Shuman, and J. J. Russo. 2004. The genomic sequence of the accidental pathogen Legionella pneumophila. Science 305:1966-1968.
10. Delcher, A. L., D. Harmon, S. Kasif, O. White, and S. L. Salzberg. 1999. Improved microbial gene identification with GLIMMER. Nucleic Acids Res. 27:4636-4641.
11. Dobrindt, U., B. Hochhut, U. Hentschel, and J. Hacker. 2004. Genomic islands in pathogenic and environmental microorganisms. Nat. Rev. Microbiol. 2:414-424.
12. Dubbels, B. L., A. A. DiSpirito, J. D. Morton, J. D. Semrau, J. N. Neto, and D. A. Bazylinski. 2004. Evidence for a copper-dependent iron transport system in the marine, magnetotactic bacterium strain MV-1. Microbiology 150:2931-2945.
13. Ewing, B., L. Hillier, M. C. Wendl, and P. Green. 1998. Base-calling of automated sequencer traces using Phred. 1. Accuracy assessment. Genome Res. 8:175-185.
14. Faure, D., R. Frederick, D. Wloch, P. Portier, M. Blot, and J. Adams. 2004. Genomic changes arising in long-term stab cultures of Escherichia coli. J. Bacteriol. 186:6437-6442.
15. Garbe, T. R., N. Suzuki, M. Inui, and H. Yukawa. 2004. Inhibitor-associated transposition events in Corynebacterium glutamicum. Mol. Genet. Genomics 271:729-741.
16. Ghanekar, K., A. McBride, O. Dellagostin, S. Thorne, R. Mooney, and J. McFadden. 1999. Stimulation of transposition of the Mycobacterium tuberculosis insertion sequence IS6110 by exposure to a microaerobic environment. Mol. Microbiol. 33:982-993.
17. Gordon, D., C. Abajian, and P. Green. 1998. Consed: a graphical tool for sequence finishing. Genome Res. 8:195-202.
18. Grünberg, K., E. C. Müller, A. Otto, R. Reszka, D. Under, 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.
19. Grünberg, K., C. Wawer, B. M. Tebo, and D. Schüler. 2001. A large gene cluster encoding several magnetosome proteins is conserved in different species of magnetotactic bacteria. Appl. Environ. Microbiol. 67:4573-4582.
20. 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.
21. Imlay, J. A. 2003. Pathways of oxidative damage. Annu. Rev. Microbiol. 57:395-418.
22. Imlay, J. A., and S. Linn. 1987. Mutagenesis and stress response induced in Escherichia coli by hydrogen peroxide. J. Bacteriol. 169:2967-2976.
23. Lesic, B., S. Bach, J. M. Ghigo, U. Dobrindt, J. Hacker, and E. Carniel. 2004. Excision of the high-pathogenicity island of Yersinia pseudotuberculosis requires the combined actions of its cognate integrase and Hef, a new recombination directionality factor. Mol. Microbiol. 52:1337-1348.
24. Lowe, T. M., and S. R. Eddy. 1997. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 25:955-964.
25. Mahillon, J., and M. Chandler. 1998. Insertion sequences. Microbiol. Mol. Biol. Rev. 62:725-774.
26. Maringanti, S., and J. A. Imlay. 1999. An intracellular iron chelator pleiotropically suppresses enzymatic and growth defects of superoxide dismutase-deficient Escherichia coli. J. Bacteriol. 181:3792-3802.
27. Michel, K. P., and E. K. Pistorius. 2004. Adaptation of the photosynthetic electron transport chain in cyanobacteria to iron deficiency: the function of IdiA and IsiA. Physiol. Plant. 120:36-50.
28. Mlouka, A., K. Comte, A.-M. Castets, C. Bouchier, and N. T. de Marsac. 2004. The gas vesicle gene cluster from Microcystis aeruginosa and DNA rearrangements that lead to loss of cell buoyancy. J. Bacteriol. 186:2355-2365.
29. Naas, T., M. Blot, W. M. Fitch, and W. Arber. 1994. Insertion sequence-related genetic variation in resting Escherichia coli K-12. Genetics 136:721-730.
30. Osborn, A. M., and D. Böltner. 2002. When phage, plasmids, and transposons collide: genomic islands, and conjugative- and mobilizable- transposons as a mosaic continuum. Plasmid. 48:202-212.
31. Pfeifer, F., and U. Blaseio. 1990. Transposition burst of the ISH27 insertion element family in Halobacterium halobium. Nucleic Acids Res. 18:6921-6925.
32. Rabus, R., M. Kube, J. Heider, A. Beck, K. Heitmann, F. Widdel, and R. Reinhardt. 2005. The genome sequence of an anaerobic aromatic-degrading denitrifying bacterium, strain EbN1. Arch. Microbiol. 183:27-36.
33. Rajeshwari, R., and R. V. Sonti. 2000. Stationary-phase variation due to transposition of novel insertion elements in Xanthomonas oryzae pv. oryzae. J. Bacteriol. 182:4797-4802.
34. Rutherford, K., J. Parkhill, J. Crook, T. Horsnell, P. Rice, M.-A. Rajandream, and B. Barrell. 2000. Artemis: sequence visualization and annotation. Bioinformatics 16:944-945.
35. Sambrook, J., and D. W. Russel. 2001. Molecular cloning: a laboratory manual, 3rd ed. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.
36. Schübbe, S., M. Kube, A. Scheffel, C. Wawer, U. Heyen, A. Meyerdierks, M. 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.
37. Schüler, D. 2004. Molecular analysis of a subcellular compartment: the magnetosome membrane in Magnetospirillum gryphiswaldense. Arch. Microbiol. 181:1-7.
38. 4 biomineralization during aerobic and microaerobic growth of Magnetospirillum gryphiswaldense. J. Bacteriol. 180:159-162.
39. Schüler, D., and E. Baeuerlein. 1996. Iron-limited growth and kinetics of iron uptake in Magnetospirillum gryphiswaldense. Arch. Microbiol. 166:301-307.
40. 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.
41. Schultheiss, D., R. Handrick, D. Jendrossek, M. Hanzlik, and D. Schüler. 2005. The presumptive magnetosome protein Mms16 is a poly(3-hydroxybutyrate) granule-bound protein (phasin) in Magnetospirillum gryphiswaldense. J. Bacteriol. 187:2416-2425.
42. Schultheiss, D., M. Kube, and D. Schüler. 2004. Inactivation of the flagellin gene flaA in Magnetospirillum gryphiswaldense results in nonmagnetotactic mutants lacking flagellar filaments. Appl. Environ. Microbiol. 70:3624-3631.
43. Schultheiss, D., and D. Schüler. 2003. Development of a genetic system for Magnetospirillum gryphiswaldense. Arch. Microbiol. 179:89-94.
44. Zambrano, M. M., D. A. Siegele, M. Almiron, A. Tormo, and R. Kolter. 1993. Microbial competition: Escherichia coli mutants that take over stationary phase cultures. Science 259:1757-1760.
45. Zinser, E. R., D. Schneider, M. Blot, and R. Kolter. 2003. Bacterial evolution through the selective loss of beneficial genes. Trade-offs in expression involving two loci. Genetics 164:1271-1277.