Accurate localization of the integration sites of two genomic islands at single-nucleotide resolution in the genome of Bacillus cereus ATCC 10987

Abstract

We have identified two genomic islands, that is, BCEGI-1 and BCEGI-2, in the genome of Bacillus cereus ATCC 10987, based on comparative analysis with Bacillus cereus ATCC 14579. Furthermore, by using the cumulative GC profile and performing homology searches between the two genomes, the integration sites of the two genomic islands were determined at single-nucleotide resolution. BCEGI-1 is integrated between 159705 bp and 198000 bp, whereas BCEGI-2 is integrated between the end of ORF BCE4594 and the start of the intergenic sequence immediately following BCE4626, that is, from 4256803 bp to 4285534 bp. BCEGI-1 harbors two bacterial Tn7 transposons, which have two sets of genes encoding TnsA, B, C, and D. It is generally believed that unlike the TnsABC+E pathway, the TnsABC+D pathway would only promote vertical transmission to daughter cells. The evidence presented in this paper, however, suggests a role of the TnsABC+D pathway in the horizontal transfer of some genomic islands.

Figure 1

The cumulative GC profile for the genomes of B. cereus ATCC 10987 and B. cereus ATCC 14579. An up jump in the cumulative GC profile indicates a sharp decrease in GC content. By comparing the cumulative GC profiles for the two closed related genomes, it is shown that most parts of the two genomes overlap, whereas two jumps (marked in red) occur in the cumulative GC profile for the genomes of B. cereus ATCC 10987, suggesting that these two regions have a relatively sharp decrease in GC content. In addition, genomic sequences surrounding these two regions are highly conserved between the two genomes. Furthermore, these two regions also have other genomic-island specific features, such as the presence of Tn7 transposon. These lines of evidence suggest that the two regions are horizontally transferred genomic islands. Refer to text for detail. In the cumulative GC profile of the genome of B. cereus ATCC 14579, the regions that correspond to the integration sites of genomic islands are indicated by arrows.

Figure 2

The GC content distribution computed based on 20 Kb windows sliding along the genomes of B. cereus ATCC 10987 and B. cereus ATCC 14579. Note that due to low resolution, the change in GC content, and the precise position of the change cannot be detected. Refer to Figure 1 for a comparison.

Figure 3

The regions that surround the genomic island BCEGI-1 and BCEGI-2 in the B. cereus ATCC 10987 genome and the corresponding regions in the genome of B. cereus ATCC 14579 are highly conserved. The same color denotes the homologous ORF's. (a) Conservation of gene orders around BCEGI-1. Briefly, except ORF's BCE0913 and BC0914, all corresponding ORF's are homologous. (b) Conservation of gene orders around BCEGI-2. All corresponding ORF's are homologous. BC denotes B. cereus ATCC 14579, whereas BCE denotes B. cereus ATCC 10987. The figure is not drawn to scale.

Figure 4

Determination of the integration sites of BCEGI-1 based on comparative analysis between B. cereus ATCC 10987 and B. cereus ATCC 14579. Besides gene orders, the intergenic sequences of the two genomes are also highly conserved. Therefore, the sequence segments that are absent in the genome of B. cereus ATCC 14579 are likely horizontally transferred. (a) Schematic diagram of BCEGI-1. The same color denotes homologous regions. The first or last codons of ORF's are marked. Integration sites are indicated. The figure is not drawn to scale. (b) Alignment of homologous intergenic sequences between the two genomes. BC denotes B. cereus ATCC 14579, whereas BCE denotes B. cereus ATCC 10987.

Figure 5

Determination of the integration sites of BCEGI-2 based on comparative analysis between B. cereus ATCC 10987 and B. cereus ATCC 14579. Besides gene orders, the intergenic sequences of the two genomes are also highly conserved. Therefore, the sequence segments that are absent in the genome of B. cereus ATCC 14579 are likely horizontally transferred. (a) Schematic diagram of BCEGI-2. The same color denotes homologous regions. The first or last codons of ORF's are marked. Integration sites are indicated. The figure is not drawn to scale. (b) Alignment of homologous intergenic sequences between the two genomes. BC denotes B. cereus ATCC 14579, whereas BCE denotes B. cereus ATCC 10987.