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Phylogenetic analysis of Shiga toxin 1 and Shiga toxin 2 genes associated with disease outbreaks.

Lee JE, Reed J, Shields MS, Spiegel KM, Farrell LD, Sheridan PP - BMC Microbiol. (2007)

Bottom Line: The analysis confirmed the Stx1 and Stx2 divergence, and showed that there is generally more sequence variation among stx2 genes than stx1.The stx1 and stx2 genes used in this phylogenetic study show sequence conservation with no significant divergence with respect to place or time.These data could indicate that Shiga toxins are experiencing purifying selection.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Biological Sciences, Idaho State University, 921 South 8th Ave,, Pocatello, ID 83209-8007, USA. james.e.lee@amedd.army.mil

ABSTRACT

Background: Shiga toxins 1 and 2 (Stx1 and Stx2) are bacteriophage-encoded proteins that have been associated with hemorrhagic colitis, hemolytic uremic syndrome and other severe disease conditions. Stx1 and Stx2 are genetically and immunologically distinct but share the same compound toxin structure, method of entry and enzymatic function.

Results: Phylogenetic analysis was performed using Stx1 and Stx2 amino acid and nucleotide sequences from 41 strains of Escherichia coli, along with known stx sequences available from GenBank. The analysis confirmed the Stx1 and Stx2 divergence, and showed that there is generally more sequence variation among stx2 genes than stx1. The phylograms showed generally flat topologies among our strains' stx1 and stx2 genes. In the stx2 gene, 39.5% of the amino acid sites display very low nonsynonymous to synonymous substitution ratios.

Conclusion: The stx1 and stx2 genes used in this phylogenetic study show sequence conservation with no significant divergence with respect to place or time. These data could indicate that Shiga toxins are experiencing purifying selection.

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Color Coded Selecton Results for stx2 Sequences. Nonsynonymous:synonymous (dN:dS) ratios using the output from the Selecton program. Shades of yellow (1 and 2) indicate a dN:dS ratio of > 1 or positive selection. Any shade of bordeaux (4–7) indicates a dN:dS ratio of < 1 or purifying selection.
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Figure 5: Color Coded Selecton Results for stx2 Sequences. Nonsynonymous:synonymous (dN:dS) ratios using the output from the Selecton program. Shades of yellow (1 and 2) indicate a dN:dS ratio of > 1 or positive selection. Any shade of bordeaux (4–7) indicates a dN:dS ratio of < 1 or purifying selection.

Mentions: The ratio non-synonymous (dN) to synonymous (dS) substitutions was used to estimate whether positive or purifying selection had occurred at each amino acid site. A nonsynonymous:synonymous (dN:dS) ratio of greater than one indicates positive selection at that amino acid site whereas a dN:dS ratio of less than one shows purifying selection. Forty percent of the amino acid sites in the full alignment showed purifying selection using the Selecton program [37]. The Stx2 A and B subunits showed 37.3% and 44.9%, respectively, of their amino acid sites were well conserved. (Figure 5)


Phylogenetic analysis of Shiga toxin 1 and Shiga toxin 2 genes associated with disease outbreaks.

Lee JE, Reed J, Shields MS, Spiegel KM, Farrell LD, Sheridan PP - BMC Microbiol. (2007)

Color Coded Selecton Results for stx2 Sequences. Nonsynonymous:synonymous (dN:dS) ratios using the output from the Selecton program. Shades of yellow (1 and 2) indicate a dN:dS ratio of > 1 or positive selection. Any shade of bordeaux (4–7) indicates a dN:dS ratio of < 1 or purifying selection.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2211750&req=5

Figure 5: Color Coded Selecton Results for stx2 Sequences. Nonsynonymous:synonymous (dN:dS) ratios using the output from the Selecton program. Shades of yellow (1 and 2) indicate a dN:dS ratio of > 1 or positive selection. Any shade of bordeaux (4–7) indicates a dN:dS ratio of < 1 or purifying selection.
Mentions: The ratio non-synonymous (dN) to synonymous (dS) substitutions was used to estimate whether positive or purifying selection had occurred at each amino acid site. A nonsynonymous:synonymous (dN:dS) ratio of greater than one indicates positive selection at that amino acid site whereas a dN:dS ratio of less than one shows purifying selection. Forty percent of the amino acid sites in the full alignment showed purifying selection using the Selecton program [37]. The Stx2 A and B subunits showed 37.3% and 44.9%, respectively, of their amino acid sites were well conserved. (Figure 5)

Bottom Line: The analysis confirmed the Stx1 and Stx2 divergence, and showed that there is generally more sequence variation among stx2 genes than stx1.The stx1 and stx2 genes used in this phylogenetic study show sequence conservation with no significant divergence with respect to place or time.These data could indicate that Shiga toxins are experiencing purifying selection.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Biological Sciences, Idaho State University, 921 South 8th Ave,, Pocatello, ID 83209-8007, USA. james.e.lee@amedd.army.mil

ABSTRACT

Background: Shiga toxins 1 and 2 (Stx1 and Stx2) are bacteriophage-encoded proteins that have been associated with hemorrhagic colitis, hemolytic uremic syndrome and other severe disease conditions. Stx1 and Stx2 are genetically and immunologically distinct but share the same compound toxin structure, method of entry and enzymatic function.

Results: Phylogenetic analysis was performed using Stx1 and Stx2 amino acid and nucleotide sequences from 41 strains of Escherichia coli, along with known stx sequences available from GenBank. The analysis confirmed the Stx1 and Stx2 divergence, and showed that there is generally more sequence variation among stx2 genes than stx1. The phylograms showed generally flat topologies among our strains' stx1 and stx2 genes. In the stx2 gene, 39.5% of the amino acid sites display very low nonsynonymous to synonymous substitution ratios.

Conclusion: The stx1 and stx2 genes used in this phylogenetic study show sequence conservation with no significant divergence with respect to place or time. These data could indicate that Shiga toxins are experiencing purifying selection.

Show MeSH
Related in: MedlinePlus