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. 2005 Dec 7:6:174.
doi: 10.1186/1471-2164年6月17日4.

Bacterial genome adaptation to niches: divergence of the potential virulence genes in three Burkholderia species of different survival strategies

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Bacterial genome adaptation to niches: divergence of the potential virulence genes in three Burkholderia species of different survival strategies

H Stanley Kim et al. BMC Genomics. .

Abstract

Background: Two closely related species Burkholderia mallei (Bm) and Burkholderia pseudomallei (Bp) are serious human health hazards and are potential bio-warfare agents, whereas another closely related species Burkholderia thailandensis (Bt) is a non-pathogenic saprophyte. To investigate the genomic factors resulting in such a dramatic difference, we first identified the Bm genes responsive to the mouse environment, and then examined the divergence of these genes in Bp and Bt.

Results: The genes down-expressed, which largely encode cell growth-related proteins, are conserved well in all three species, whereas those up-expressed, which include potential virulence genes, are less well conserved or absent notably in Bt. However, a substantial number of up-expressed genes is still conserved in Bt. Bm and Bp further diverged from each other in a small number of genes resulting from unit number changes in simple sequence repeats (ssr) in the homologs.

Conclusion: Our data suggest that divergent evolution of a small set of genes, rather than acquisition or loss of pathogenic islands, is associated with the development of different life styles in these bacteria of similar genomic contents. Further divergence between Bm and Bp mediated by ssr changes may reflect different adaptive processes of Bm and Bp fine-tuning into their host environments.

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Figures

Figure 1
Figure 1
Expression of B. mallei (Bm) genes in vivo profiled in contrast to that in cultures and to Bm genomic DNA. A. Heat map representation of gene expression profiles of the three distinct groups and a description of each hybridization pair. The two bars in the box at the top indicate colors corresponding to the range of the observed expression ratios on a log2 scale for the data generated with two different references. B. Over- or under-representation of role categories in the in vivo-responsive genes. Percent changes in the proportion of each role category relative to its original proportion in the genome are shown.
Figure 2
Figure 2
Comparative genomic analyses of B. mallei, B. pseudomallei, and B. thailandensis with the whole genomes and with in vivo-responsive genes. The data are based on the TBLASTN scores generated with Bm proteome and nucleotide sequences of Bp or Bt. A. Comparison between B. mallei and B. pseudomallei. Genes of both % identity and % length equal to or above 80 and all below the cut off as a group are shown with % distribution. Comparison statistics (Mean and Standard Deviation) are also shown in the table present inside the graph. The blue, red, and green colors are used in the table to match the bars in the graph that they have statistics for. B. Comparison between B. mallei and B. thailandensis.
Figure 3
Figure 3
Comparison among B. mallei, B. pseudomallei, and B. thailandensis with a divergence cut-off of two-times of standard deviation from the mean values of identity and length match. Venn diagrams show the numbers of genes common or diverged or unique to each genome. Genes in the diagrams are shown in Additional files 4, 5 and 6. A. Comparisons generated based on the TBLASTN scores with the proteome of one genome to the nucleotide sequences of other genomes. Segments labeled 1, 2, 3, 4 are based on the Bm proteome, while segments 5 and 6 are based on the Bp proteome and segment 7 is based on the Bt proteome. B. Comparisons with in vivo-responsive group 1 and 3 genes and group 2 genes (see Figure 1).
Figure 4
Figure 4
Comparison of the Type III Secretion Systems (TTSSs) and the surrounding regions in B. mallei (Bm), B. pseudomallei (Bp), and B. thailandensis (Bt). The orthologous genes in the three species are denoted with connecting lines. A. Comparison of TTSS-3 locus among the three species. The % amino acid identity was determined using TBLASTN from Bp proteins, and is color coded accordingly. B. Comparison of TTSS-2 and its vicinity. Large deletions in the genes coding for non ribosomal peptide synthases (NRPSs) in Bm and Bt are shown. Two frame shift mutations in the two genes in the TTSS-2 of Bm also are shown. C. Comparison of the regions around TTSS-1. The fragment containing TTSS-1 and the surrounding genes that are only present in Bp, and the replacement fragments of this in Bt and Bm are shown.
Figure 5
Figure 5
Comparison of the wcb capsule synthesis region in B. mallei (Bm), B. pseudomallei (Bp), and B. thailandensis (Bt). The orthologous genes in the three species are denoted with connecting lines. The % amino acid identity was determined using TBLASTN, and is color coded accordingly.

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