Complete genomic structure of the bloom-forming toxic cyanobacterium microcystis aeruginosa NIES-843

DNA Research

Volumn 14, Issue 6, 2007, Pages 247-256

  Kaneko, Takakazu ^a   Nakajima, Nobuyoshi ^b   Okamoto, Shinobu ^a   Suzuki, Iwane ^c   Tanabe, Yuuhiko ^b   Tamaoki, Masanori ^b   Nakamura, Yasukazu ^a   Kasai, Fumie ^b   Watanabe, Akiko ^a   Kawashima, Kumiko ^a   Kishida, Yoshie ^a   Ono, Akiko ^a   Shimizu, Yoshimi ^a   Takahashi, Chika ^a   Minami, Chiharu ^a   Fujishiro, Tsunakazu ^a   Kohara, Mitsuyo ^a   Katoh, Midori ^a   Nakazaki, Naomi ^a   Nakayama, Shinobu ^a   Yamada, Manabu ^a   Tabata, Satoshi ^a   Watanabe, Makoto M ^c   more..

^a KAZUSA DNA RESEARCH INSTITUTE   (Japan)

^b NATIONAL INSTITUTE FOR ENVIRONMENTAL STUDIES   (Japan)

^c UNIVERSITY OF TSUKUBA   (Japan)

Author keywords

Cyanobacterium; Genome sequence; M. aeruginosa; Microcystin; Water bloom

Indexed keywords

BACTERIAL PROTEIN;

ARTICLE; BACTERIAL GENOME; COMPARATIVE STUDY; DNA BASE COMPOSITION; DNA SEQUENCE; GENETICS; MICROCYSTIS; MOLECULAR GENETICS; MULTIGENE FAMILY; NUCLEOTIDE SEQUENCE; PROTEIN TERTIARY STRUCTURE;

BACTERIAL PROTEINS; BASE COMPOSITION; BASE SEQUENCE; GENOME, BACTERIAL; MICROCYSTIS; MOLECULAR SEQUENCE DATA; MULTIGENE FAMILY; PROTEIN STRUCTURE, TERTIARY; SEQUENCE ANALYSIS, DNA;

EID: 40949129063     PISSN: 13402838     EISSN: 17561663     Source Type: Journal    
DOI: 10.1093/dnares/dsm026     Document Type: Article

References (57)

1. Codd, G. A., Lindsay, J., Young, F. M., Morrison, L. F. and Metcalf, J. S. 2005, In: Huisman, J., Matthijs, H. C. P. and Visser, P. M. (eds.), Harmful Cyanobacteria, Netherlands: Springer, pp. 1-23.
2. Bister, B., Simone Keller, S., Baumann, H. I., et al. 2004, Cyanopeptolin 963A, a chymotrypsin inhibitor of Microcystis PCC 7806, J. Nat. Prod., 67, 1755-1757.
3. Holt, J. G., Krieg, N. R., Sneath, P. H. A., Staley, J. T. and Williams, S. T. 1994, In: Hensyl, W. R. (ed.), Bergey's Manual of Determinative Bacteriology, 9th Ed., Baltimore: Williams & Wilkins, pp. 377-425.
4. Komárek, J. 1991, A review of water-bloom forming Microcystis species, with regard to populations from Japan, Arch. Hydrobiol. Suppl. Algol. Stud., 64, 115-127.
5. Watanabe, M. 1996, In: Watanabe, M. F., Harada, K., Carmichael, W. W. and Fujiki, H. (eds.), Toxic Microcystis, Boca Raton: CRC Press, pp. 13-34.
6. Otsuka, S., Suda, S., Li, R., Matsumoto, S. and Watanabe, M. M. 2000, Morphological variability of colonies of Microcystis morphospecies in culture, J. Gen. Appl. Microbiol., 46, 39-50.
7. Otsuka, S., Suda, S., Li, R., Watanabe, M., Oyaizu, H., Matsumoto, S. and Watanabe, M. M. 1998, 16S rDNA sequences and phylogenetic analyses of Microcystis strains with and without phycoerythrin, FEMS Microbiol. Lett., 164, 119-124.
8. Otsuka, S., Suda, S., Li, R., et al. 1999, Phylogenetic relationships between toxic and non-toxic strains of the genus Microcystis based on 16S to 23S internal transcribed spacer sequences, FEMS Microbiol. Lett., 172, 15-21.
9. Otsuka, S., Suda, S., Li, R., et al. 1999, Characterization of morphospecies and strains of the genus Microcystis (Cyanobacteria) for a reconsideration of speceis classification, Phycol. Res., 47, 189-197.
10. Wayne, L. G., Brenner, D. J., Colwell, R. R., et al. 1987, International Committee on Systematic Bacteriology. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics, Int. J. Syst. Bacteriol., 37, 463-464.
11. Otsuka, S., Suda, S., Shibata, S., Oyaizu, H., Matsumoto, S. and Watanabe, M. M., 2001, A proposal for the unification of five species of the cyanobacterial genus Microcystis Kützing ex Lemmermann 1907 under the Rules of the Bacteriological Code, Int. J. Syst. Evol. Microbiol. 51, 873-879.
12. Kaneko, T., Nakamura, Y., Wolk, C. P., et al. 2001, Complete genomic sequence of the filamentous nitrogen-fixing cyanobacterium Anabaena sp. strain PCC 7120, DNA Res., 8, 205-213.
13. Lowe, T. M. and Eddy, S. R. 1997, tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence, Nucleic Acids Res., 25, 955-964.
14. Lagesen, K., Hallin, P., Rødland, E. A., Staerfeldt, H. H., Rognes, T. and Ussery, D. W. 2007, RNAmmer: consistent and rapid annotation of ribosomal RNA genes, Nucleic Acids Res., 35, 3100-3108.
15. Delcher, A. L., Harmon, D., Kasif, S., White, O. and Salzberg, S. L. 1999, Improved microbial gene identification with GLIMMER, Nucleic Acids Res., 27, 4636-4641.
16. Altschul, S. F., Madden, T. L., Schaffer, A. A., et al. 1997, Gapped BLAST and PSI-BLAST: a new generation of protein database search programs, Nucleic Acids Res., 25, 3389-3402.
17. Mulder, N. J., Apweiler, R., Attwood, T. K., et al. 2007, New developments in the InterPro database, Nucleic Acids Res., 35, D224-D228.
18. Tatusov, R. L., Fedorova, N. D., Jackson, J. D., et al. 2003, The COG database: an updated version includes eukaryotes, BMC Bioinformatics, 4, 41.
19. Bao, Z. and Eddy, S. R. 2002, Automated de novo identification of repeat sequence families in sequenced genomes, Genome Res., 12, 1269-1276.
20. Kaneko, T., Sato, S., Kotani, H., et al. 1996, Sequence analysis of the genome of the unicellular cyanobacterium Synechocystis sp. strain PCC6803. II. Sequence determination of the entire genome and assignment of potential protein-coding regions, DNA Res., 3, 109-136.
21. Gupta, A., Morby, A. P., Turner, J. S., Whitton, B. A. and Robinson, N. J. 1993, Deletion within the metallothionein locus of cadmium-tolerant Synechococcus PCC 6301 involving a highly iterated palindrome (HIP1), Mol. Microbiol., 7, 189-195.
22. Kaneko, T., Nakamura, Y., Sasamoto, S., et al. 2003, Structural analysis of four large plasmids harboring in a unicellular cyanobacterium, Synechocystis sp. PCC 6803, DNA Res., 10, 221-228.
23. Nakamura, Y., Kaneko, T., Sato, S., et al. 2002, Complete genome structure of the thermophilic cyanobacterium Thermosynechococcus elongatus BP-1, DNA Res., 9, 123-130.
24. Nakamura, Y., Kaneko, T., Sato, S., et al. 2003, Complete genome structure of Gloeobacter violaceus PCC 7421, a cya-nobacterium that lacks thylakoids, DNA Res., 10, 137-145.
25. Mlouka, A., Comte, K. and Tandeau de Marsac, N. 2004, Mobile DNA elements in the gas vesicle gene cluster of the planktonic cyanobacteria Microcystis aeruginosa, FEMS Microbiol. Lett., 237, 27-34.
26. Bureau, T. E., Ronald, P. C. and Wessler, S. R., 1996, A computer-based systematic survey reveals the predominance of small inverted-repeat elements in wild-type rice genes. Proc. Natl. Acad. Sci. USA, 93, 8524-8529.
27. Nishizawa, T., Asayama, M., Fujii, K., Harada, K. and Shirai, M., 1999, Genetic analysis of the peptide synthetase genes for a cyclic heptapeptide microcystin in Microcystis spp., J. Biochem., 126, 520-529.
28. Dittmann, E. and Börner, T. 2005, Genetic contributions to the risk assessment of microcystin in the environment, Toxicol. Appl. Pharmacol., 203, 192-200.
29. Nishizawa, T., Ueda, A., Asayama, M., et al. 2000, Polyketide synthase gene coupled to the peptide synthetase module involved in the biosynthesis of the cyclic heptapep-tide microcystin, J. Biochem., 127, 779-789.
30. Tillett, D., Dittmann, E., Erhard, M., von Döhren, H., Börner, T. and Neilan, B. A. 2000, Structural organization of microcystin biosynthesis in Microcystis aeruginosa PCC 7806: an integrated peptide-polyketide synthetase system, Chem. Biol., 7, 753-764.
31. Tanabe, Y., Kasai, F. and Watanabe, M. M., 2007, Multilocus sequence typing (MLST) reveals high genetic diversity and clonal population structure of the toxic cyano-bacterium Microcystis aeruginosa, Microbiology, 153, 3695-3703.
32. Mikalsen, B., Boison, G., Skulberg, O. M., et al., 2003, Natural variation in the microcystin synthetase operon mcyABC and impact on microcystin production in Microcystis strains, J. Bacteriol., 185, 2774-2785.
33. Tanabe, Y., Kaya, K. and Watanabe, M. M. 2004, Evidence for recombination in the microcystin synthetase (mcy) genes of toxic cyanobacteria Microcystis spp., J. Mol. Evol., 58, 633-641.
34. Schneider, A. and Marahiel, M. A. 1998, Genetic evidence for a role of thioesterase domains, integrated in or associated with peptide synthetases, in non-ribosomal peptide biosynthesis in Bacillus subtilis, Arch. Microbiol., 169, 404-410.
35. Christiansen, G., Fastner, J., Erhard, M., Börner, T. and Dittmann, E. 2003, Microcystin Biosynthesis in Planktothrix: Genes, Evolution, and Manipulation, J. Bacteriol., 185, 564-572.
36. Mootz, H. D. and Marahiel, M. A. 1997, Biosynthetic systems for nonribosomal peptide antibiotic assembly, Curr. Opin. Chem. Biol., 1, 543-551.
37. Copp, J. N. and Neilan, B. A. 2006, The phosphopantetheinyl transferase superfamily: phylogenetic analysis and functional implications in cyanobacteria, Appl. Environ. Microbiol., 72, 2298-2305.
38. Tooming-Klunderud, A., Rohrlack, T., Shalchian-Tabrizi, K., Kristensen, T. and Jakobsen, K. S. 2007, Structural analysis of a non-ribosomal halogenated cyclic peptide and its putative operon from Microcystis: implications for evolution of cyanopeptolins, Microbiology, 153, 1382-1393.
39. Mlouka, A., Comte, K., Castets, A-M., Bouchier, C. and Tandeau de Marsac, N. 2004, The gas vescle gene cluster from Microcystis aeruginosa and DNA rearrangements that led to loss of cell buoyancy, J. Bacteriol., 186, 2355-2365.
40. Walsby, A. E. 1994, Gas vesicles, Microbiol. Rev., 58, 94-144.
41. Beard, S. J., Handley, B. A., Hayes, P. K. and Walsby, A. E. 1999, The diversity of gas vesicle genes in Planktothrix rubescens from Lake Zürich, Microbiology, 145, 2757-2768.
42. Walsby, A. E. and Hayes, P. K. 1988, The minor cyanobacterial gas vescle protein, GVPc, is attached to the outer surface of the gas vesicle, J. Gen. Microbiol., 134, 2647-2657.
43. Dunton, P. G. and Walsby, A. E. 2005, The diameter and critical collapse pressure of gas vesicles in Microcystis are correlated with GvpCs of different length, FEMS Microbiol. Lett., 247, 37-43.
44. Minezaki, Y., Homma, K. and Nishikawa, K. 2005, Genome-wide survey of transcription factors in prokaryotes reveals many bacteria-specific families not found in archaea, DNA Res., 12, 269-280.
45. Mizuno, T., Kaneko, T. and Tabata, S. 1996, Compilation of all genes encoding bacterial two-component signal transducers in the genome of the cyanobacterium, Synechocystis sp. strain PCC 6803, DNA Res., 3, 407-414.
46. Ashby, M. K., Houmard, J. and Mullineaux, C. W. 2002, The ycf27 genes from cyanobacteria and eukaryotic algae: distribution and implications for chloroplast evolution, FEMS Microbiol. Lett., 214, 25-30.
47. Suzuki, S., Ferjani, A., Suzuki, I. and Murata, N. 2004, The SphS-SphR two component system is the exclusive sensor for the induction of gene expression in response to phosphate limitation in Synechocystis, J. Biol. Chem., 279, 13234-13240.
48. Juntarajumnong, W., Hirani, T. A., Simpson, J. M., Incharoensakdi, A. and Eaton-Rye, J. J. 2007, Phosphate sensing in Synechocystis sp. PCC 6803: SphU and the SphS-SphR two-component regulatory system, Arch. Microbiol., 188, 389-402.
49. Vega-Palas, M. A., Madueno, F., Herrero, A. and Flores, E. 1990, Identification and cloning of a regulatory gene for nitrogen assimilation in the cyanobacterium Synechococcus sp. strain PCC 7942, J. Bacteriol., 172, 643-647.
50. Aichi, M., Takatani, N. and Omata, T. 2001, Role of NtcB in activation of nitrate assimilation genes in the cyanobac-terium Synechocystis sp. strain PCC 6803, J. Bacteriol., 183, 5840-5847.
51. Maier, U. G., Fraunholz, M., Zauner, S., Penny, S. and Douglas, S. 2000, A nucleomorph-encoded CbbX and the phylogeny of RuBisCo regulators, Mol. Biol. Evol., 17, 576-583.
52. 2-concentrating mechanism in the cyanobacterium Synechocystis sp. strain PCC6803, Plant Physiol., 132, 218-229.
53. Yoshimura, H., Hisabori, T., Yanagisawa, S. and Ohmori, M. 2000, Identification and characterization of a novel cAMP receptor protein in the cyanobacterium Synechocystis sp. PCC 6803, J. Biol. Chem., 275, 6241-6245.
54. Nakamoto, H., Suzuki, M. and Kojima, K. 2003, Targeted inactivation of the hrcA repressor gene in cyanobacteria, FEBS Lett., 549, 57-62.
55. Thelwell, C., Robinson, N. J. and Turner-Cavet, J. S. 1998, An SmtB-like repressor from Synechocystis PCC 6803 regulates a zinc exporter, Proc. Natl. Acad. Sci. USA, 95, 10728-10733.
56. Kloft, N., Rasch, G. and Forchhammer, K. 2005, Protein phosphatase PphA from Synechocystis sp. PCC 6803: the physiological framework of PII-P dephosphorylation, Microbiology, 151, 1275-1283.
57. Roberts, R. J., Vincze, T., Posfai, J. and Macelis, D. 2007, REBASE - enzymes and genes for DNA restriction and modification, Nucleic Acids Res. 35, D269-D270.