Abstract
We report a draft sequence of the genome of Oscillatoria sp. PCC 6506, a cyanobacterium that produces anatoxin-a and homoanatoxin-a, two neurotoxins, and cylindrospermopsin, a cytotoxin. Beside the clusters of genes responsible for the biosynthesis of these toxins, we have found other clusters of genes likely involved in the biosynthesis of not-yet-identified secondary metabolites.
The presence in the environment of cyanobacteria producing toxins represents a risk for human and animal health (5). It is thus important to develop methodologies to detect these toxic microorganisms in water reservoirs, and so far, PCR-based amplification of genes responsible for the biosynthesis of these toxins is the best method (1). We have been interested in the study of cyanobacteria producing the neurotoxins anatoxin-a and homoanatoxin-a (2, 17, 18). Our goals were first to identify the genes responsible for the biosynthesis of these toxins and to deepen our knowledge of this interesting group of bacteria. For that, we chose Oscillatoria sp. PCC 6506 (4, 6, 14), a filamentous benthic cyanobacterium, as our model microorganism and initiated the sequencing of its genome.
Whole-genome shotgun sequencing of Oscillatoria sp. PCC 6506 was performed using the 454 technology (GATC, Konstanz, Germany), giving 677,304 reads, with a total number of 164 megabases, representing an estimated coverage of 24. Assembly yielded 419 contigs consisting of 6,729,249 bases with a G+C content of 43.40%. Automatic annotation of this genome using the MaGe pipeline system (16) predicted 6,007 coding sequences (CDS), 61 fragments of CDS, and 84 genes coding for RNA (4 rRNA genes, 70 tRNA genes, and 10 small noncoding RNAs [ncRNAs]).
Oscillatoria sp. PCC 6506 is an aerobic photosynthetic and diazotrophic cyanobacterium that shows transient and dispersed gas vesicles (4, 6). We found 37 genes coding for proteins involved in photosynthesis and the nif gene cluster, responsible for nitrogen fixation. However, we could not identify any gene coding for a hydrogenase (15), as for Synechococcus sp. BG043511 (8). Four genes were annotated as gas vesicle protein (gvp) genes (13).
Oscillatoria sp. PCC 6506 produces anatoxin-a and homoanatoxin-a, and we recently identified the ana cluster of genes, responsible for the biosynthesis of these alkaloids (3, 10, 11). We also identified the cluster of genes (cyr) responsible for the biosynthesis of cylindrospermopsin (9, 12). Cyanobacteria are known to produce a wide range of secondary metabolites (7), and 3.7% of the total annotated CDS in this genome were dedicated to secondary metabolism. We identified, beside the ana and cyr clusters, four other clusters of genes containing polyketide synthase and nonribosomal peptide synthase coding genes, likely involved in the biosynthesis of secondary metabolites.
We found 51 transposase genes in the Oscillatoria sp. PCC 6506 genome, some close to the biosynthetic gene clusters identified, suggesting horizontal gene transfer events.
In conclusion, we present here the sequence of the first genome of an Oscillatoria cyanobacterium strain, a very common genus found in the environment, and the first genome of a neurotoxin-producing cyanobacterium.
Nucleotide sequence accession numbers.
This genome has been deposited in the DDBJ/EMBL/GenBank databases (accession no. CACA01000001 to CACA01000377). This first version contains 377 contigs over 419, because we removed the 42 contigs for which the size was less than 500 bp. MaGe annotation data will be made available to the public at the MaGe CyanoScope website (https://www.genoscope.cns.fr/agc/microscope/about/collabprojects.php?P_id=68) at the same time as the DDBJ/EMBL/GenBank release.
Acknowledgments
This work was supported by the Institut Pasteur, the Ecole Nationale Supérieure de Chimie de Paris, the Centre National de la Recherche Scientifique (URA 2172 and UMR7223), the INSERM grant Multiorganismes from Aventis Pharma (Groupe Sanofi-Aventis) and Bayer Pharma, and by the Agence Française de Sécurité Sanitaire de l'Environnement et du Travail, grant Environnement et Santé.
We thank R. Rippka for providing the axenic strain Oscillatoria sp. PCC 6506 and for valuable advice concerning the cultures of cyanobacteria. N. Tandeau de Marsac, I. Iteman, and S. Cadel-Six are all thanked for their constant support and for valuable scientific discussions during the course of this work. We thank Z. Rouy for helping us during the submission of the genome.
Footnotes
Published ahead of print on 30 July 2010.
REFERENCES
- 1.Burns, B. P., M. L. Saker, M. C. Moffitt, and B. A. Neilan. 2004. Molecular detection of genes responsible for cyanobacterial toxin production in the genera Microcystis, Nodularia, and Cylindrospermopsis. Methods Mol. Biol. 268:213-222. [DOI] [PubMed] [Google Scholar]
- 2.Cadel-Six, S., C. Peyraud-Thomas, L. Brient, N. Tandeau de Marsac, R. Rippka, and A. Méjean. 2007. Different genotypes of anatoxin-producing cyanobacteria coexist in the Tarn River, France. Appl. Environ. Microbiol. 73:7605-7614. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 3.Cadel-Six, S., I. Iteman, C. Peyraud-Thomas, S. Mann, O. Ploux, and A. Méjean. 2009. Identification of a polyketide synthase coding sequence specific for anatoxin-a-producing Oscillatoria cyanobacteria. Appl. Environ. Microbiol. 75:4909-4912. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 4.Castenholz, R. W., R. Rippka, M. Herdman, and A. Wilmotte. 2001. Subsection III, order Oscillatoriales (Elenkin 1934), p. 539-562. In D. R. Boone, R. W. Castenholz, and G. M. Garrity (ed.), Bergey's manual of systematic bacteriology, 2nd ed., vol. 1. The Archaea and the deeply branching and phototrophic bacteria. Springer Verlag, New York, NY. [Google Scholar]
- 5.Chorus, I., and J. Bartram (ed.). 1999. Toxic cyanobacteria in water: a guide to their public health consequences, monitoring and management. Spon Press, London, United Kingdom.
- 6.Herdman, M., I. Iteman, and R. Rippka. 2005. Catalogue of cyanobacterial strains, 2nd ed. Institut Pasteur, Paris, France.
- 7.Kalaitzis, J. A., F. M. Lauro, and B. A. Neilan. 2009. Mining cyanobacterial genomes for genes encoding complex biosynthetic pathways. Nat. Prod. Rep. 26:1447-1465. [DOI] [PubMed] [Google Scholar]
- 8.Ludwig, M., R. Schulz-Friedrich, and J. Appel. 2006. Occurrence of hydrogenases in cyanobacteria and anoxygenic photosynthetic bacteria: implications for the phylogenetic origin of cyanobacterial and algal hydrogenases. J. Mol. Evol. 63:758-768. [DOI] [PubMed] [Google Scholar]
- 9.Mazmouz, R., F. Chapuis-Hugon, S. Mann, V. Pichon, A. Méjean, and O. Ploux. 2010. Biosynthesis of cylindrospermopsin and 7-epicylindrospermopsin in Oscillatoria PCC 6506; identification of the gene cluster and toxin analysis. Appl. Environ. Microbiol. 76:4943-4949. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 10.Méjean, A., S. Mann, G. Vassiliadis, B. Lombard, D. Loew, and O. Ploux. 2010. In vitro reconstitution of the first steps of anatoxin-a biosynthesis in Oscillatoria PCC 6506: from free L-proline to acyl carrier protein bound dehydroproline. Biochemistry 49:103-113. [DOI] [PubMed] [Google Scholar]
- 11.Méjean, A., S. Mann, T. Maldiney, G. Vassiliadis, O. Lequin, and O. Ploux. 2009. Evidence that biosynthesis of the neurotoxic alkaloids anatoxin-a and homoanatoxin-a in the cyanobacterium Oscillatoria PCC 6506 occurs on a modular polyketide synthase initiated by L-proline. J. Am. Chem. Soc. 131:7512-7513. [DOI] [PubMed] [Google Scholar]
- 12.Mihali, T. K., R. Kellmann, J. Muenchhoff, K. D. Barrow, and B. A. Neilan. 2008. Characterization of the gene cluster responsible for cylindrospermopsin biosynthesis. Appl. Environ. Microbiol. 74:716-722. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 13.Mlouka, A., K. Comte, A. M. Castets, C. Bouchier, and N. Tandeau 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. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 14.Rippka, R. 1988. Isolation and purification of cyanobacteria. Methods Enzymol. 167:3-27. [DOI] [PubMed] [Google Scholar]
- 15.Tamagnini, P., E. Leitão, P. Oliveira, D. Ferreira, F. Pinto, D. J. Harris, T. Heidorn, and P. Lindblad. 2007. Cyanobacterial hydrogenases: diversity, regulation and applications. FEMS Microbiol. Rev. 31:692-720. [DOI] [PubMed] [Google Scholar]
- 16.Vallenet, D., L. Labarre, Z. Rouy, V. Barbe, S. Bocs, S. Cruveiller, A. Lajus, G. Pascal, C. Scarpelli, and C. Médigue. 2006. MaGe: a microbial genome annotation system supported by synteny results. Nucleic Acids Res. 34:53-65. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 17.van Apeldoorn, M. E., H. P. van Egmond, G. J. Speijers, and G. J. Bakker. 2007. Toxins of cyanobacteria. Mol. Nutr. Food Res. 51:7-60. [DOI] [PubMed] [Google Scholar]
- 18.Wonnacott, S., and T. Gallagher. 2006. The chemistry and pharmacology of anatoxin-a and related homotropanes with respect to nicotinic acetylcholine receptors. Mar. Drugs 4:228-254. [Google Scholar]