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

Abstract

The nucleotide sequence of the complete genome of a cyanobacterium, Microcystis aeruginosa NIES-843, was determined. The genome of M. aeruginosa is a single, circular chromosome of 5,842,795 base pairs (bp) in length, with an average GC content of 42.3%. The chromosome comprises 6312 putative protein-encoding genes, two sets of rRNA genes, 42 tRNA genes representing 41 tRNA species, and genes for tmRNA, the B subunit of RNase P, SRP RNA, and 6Sa RNA. Forty-five percent of the putative protein-encoding sequences showed sequence similarity to genes of known function, 32% were similar to hypothetical genes, and the remaining 23% had no apparent similarity to reported genes. A total of 688 kb of the genome, equivalent to 11.8% of the entire genome, were composed of both insertion sequences and miniature inverted-repeat transposable elements. This is indicative of a plasticity of the M. aeruginosa genome, through a mechanism that involves homologous recombination mediated by repetitive DNA elements. In addition to known gene clusters related to the synthesis of microcystin and cyanopeptolin, novel gene clusters that may be involved in the synthesis and modification of toxic small polypeptides were identified. Compared with other cyanobacteria, a relatively small number of genes for two component systems and a large number of genes for restriction-modification systems were notable characteristics of the M. aeruginosa genome.

Figure 1

Schematic representation of the circular chromosome of M. aeruginosa. The scale indicates location in bp, starting with the initiation codon (ATG) of MAE00010, an ortholog of slr0611 in Synechocystis sp. PCC 6803. The bars in the outermost and the second circles show the positions of the putative protein-encoding genes in the clockwise and counter-clockwise directions, respectively. The putative genes are represented by 20 color codes, based on COG assignments (Supplementary Fig. 3). The bars in the third and fourth circles indicate the positions of MITEs (in red) and ISs (in blue). The innermost circles with scales show the percent average GC content calculated using a window size of 10 kb. The sequences as well as the gene information shown in this paper are available in CyanoBase (http://bacteria.kazusa.or.jp/cyano/). The sequence data analyzed in this study has been registered in DDBJ/GenBank/EMBL under accession number AP009552.

Figure 2

Distribution of IS families in cyanobacteria and Escherichia coli. Bars indicate the distribution of known IS families, which are represented by 18 color codes. Mae, Microcystis aeruginosa NIES-843; Syn, Synechocystis sp. PCC 6803; Ana, Anabaena sp. PCC 7120; Tel, Themosynechococcus elongates BP-1; Gvi, Gloeobacter violaceus PCC 7421; Eco, Escherichia coli K-12.