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Contrasting evolutionary patterns of spore coat proteins in two Bacillus species groups are linked to a difference in cellular structure.

Qin H, Driks A - BMC Evol. Biol. (2013)

Bottom Line: We then performed genome-wide comparisons of the nonsynonymous/synonymous substitution rate ratio, dN/dS, and found contrasting patterns: Coat proteins have significantly higher dN/dS in the B. subtilis-group genomes, but not in the B. cereus-group genomes.We further corroborated this contrast by examining changes of dN/dS within gene trees, and found that some coat protein gene trees have significantly different dN/dS between the B subtilis-clade and the B. cereus-clade.We speculate that the absence of the exosporium in the B. subtilis spore coat effectively lifted a structural constraint that has led to relaxed negative selection pressure on the outer coat.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Biology, Spelman College, Atlanta, GA 30314, USA. hqin@spelman.edu.

ABSTRACT

Background: The Bacillus subtilis-group and the Bacillus cereus-group are two well-studied groups of species in the genus Bacillus. Bacteria in this genus can produce a highly resistant cell type, the spore, which is encased in a complex protective protein shell called the coat. Spores in the B. cereus-group contain an additional outer layer, the exosporium, which encircles the coat. The coat in B. subtilis spores possesses inner and outer layers. The aim of this study is to investigate whether differences in the spore structures influenced the divergence of the coat protein genes during the evolution of these two Bacillus species groups.

Results: We designed and implemented a computational framework to compare the evolutionary histories of coat proteins. We curated a list of B. subtilis coat proteins and identified their orthologs in 11 Bacillus species based on phylogenetic congruence. Phylogenetic profiles of these coat proteins show that they can be divided into conserved and labile ones. Coat proteins comprising the B. subtilis inner coat are significantly more conserved than those comprising the outer coat. We then performed genome-wide comparisons of the nonsynonymous/synonymous substitution rate ratio, dN/dS, and found contrasting patterns: Coat proteins have significantly higher dN/dS in the B. subtilis-group genomes, but not in the B. cereus-group genomes. We further corroborated this contrast by examining changes of dN/dS within gene trees, and found that some coat protein gene trees have significantly different dN/dS between the B subtilis-clade and the B. cereus-clade.

Conclusions: Coat proteins in the B. subtilis- and B. cereus-group species are under contrasting selective pressures. We speculate that the absence of the exosporium in the B. subtilis spore coat effectively lifted a structural constraint that has led to relaxed negative selection pressure on the outer coat.

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Histograms of orthologous hits for B. subtilis inner and outer coat proteins. The number of orthologous hits for each coat protein in the B. cereus-group is calculated as the sum of the hits in B. anthracis, B. thuringiensis, B. cereus, and B. weihenstephanensis. Each bin represents the number of B. subtilis coat proteins with the indicated number of orthologous hits.
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Figure 4: Histograms of orthologous hits for B. subtilis inner and outer coat proteins. The number of orthologous hits for each coat protein in the B. cereus-group is calculated as the sum of the hits in B. anthracis, B. thuringiensis, B. cereus, and B. weihenstephanensis. Each bin represents the number of B. subtilis coat proteins with the indicated number of orthologous hits.

Mentions: We are aware that the test in Table 1 can be influenced by the partitioning of coat proteins into conserved and labile categories. To avoid this caveat, we examined the orthologous hits directly. For each coat protein, we counted the number of B. cereus group species that contains an orthologous hit based on their phylogenetic profile in Figure 3. Histograms of these counts are plotted side-by-side for inner and out proteins in Figure 4. The inner coat proteins have significantly more orthologous hits than the outer coat proteins (Wilcoxon test, p = 0.039).


Contrasting evolutionary patterns of spore coat proteins in two Bacillus species groups are linked to a difference in cellular structure.

Qin H, Driks A - BMC Evol. Biol. (2013)

Histograms of orthologous hits for B. subtilis inner and outer coat proteins. The number of orthologous hits for each coat protein in the B. cereus-group is calculated as the sum of the hits in B. anthracis, B. thuringiensis, B. cereus, and B. weihenstephanensis. Each bin represents the number of B. subtilis coat proteins with the indicated number of orthologous hits.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4219348&req=5

Figure 4: Histograms of orthologous hits for B. subtilis inner and outer coat proteins. The number of orthologous hits for each coat protein in the B. cereus-group is calculated as the sum of the hits in B. anthracis, B. thuringiensis, B. cereus, and B. weihenstephanensis. Each bin represents the number of B. subtilis coat proteins with the indicated number of orthologous hits.
Mentions: We are aware that the test in Table 1 can be influenced by the partitioning of coat proteins into conserved and labile categories. To avoid this caveat, we examined the orthologous hits directly. For each coat protein, we counted the number of B. cereus group species that contains an orthologous hit based on their phylogenetic profile in Figure 3. Histograms of these counts are plotted side-by-side for inner and out proteins in Figure 4. The inner coat proteins have significantly more orthologous hits than the outer coat proteins (Wilcoxon test, p = 0.039).

Bottom Line: We then performed genome-wide comparisons of the nonsynonymous/synonymous substitution rate ratio, dN/dS, and found contrasting patterns: Coat proteins have significantly higher dN/dS in the B. subtilis-group genomes, but not in the B. cereus-group genomes.We further corroborated this contrast by examining changes of dN/dS within gene trees, and found that some coat protein gene trees have significantly different dN/dS between the B subtilis-clade and the B. cereus-clade.We speculate that the absence of the exosporium in the B. subtilis spore coat effectively lifted a structural constraint that has led to relaxed negative selection pressure on the outer coat.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Biology, Spelman College, Atlanta, GA 30314, USA. hqin@spelman.edu.

ABSTRACT

Background: The Bacillus subtilis-group and the Bacillus cereus-group are two well-studied groups of species in the genus Bacillus. Bacteria in this genus can produce a highly resistant cell type, the spore, which is encased in a complex protective protein shell called the coat. Spores in the B. cereus-group contain an additional outer layer, the exosporium, which encircles the coat. The coat in B. subtilis spores possesses inner and outer layers. The aim of this study is to investigate whether differences in the spore structures influenced the divergence of the coat protein genes during the evolution of these two Bacillus species groups.

Results: We designed and implemented a computational framework to compare the evolutionary histories of coat proteins. We curated a list of B. subtilis coat proteins and identified their orthologs in 11 Bacillus species based on phylogenetic congruence. Phylogenetic profiles of these coat proteins show that they can be divided into conserved and labile ones. Coat proteins comprising the B. subtilis inner coat are significantly more conserved than those comprising the outer coat. We then performed genome-wide comparisons of the nonsynonymous/synonymous substitution rate ratio, dN/dS, and found contrasting patterns: Coat proteins have significantly higher dN/dS in the B. subtilis-group genomes, but not in the B. cereus-group genomes. We further corroborated this contrast by examining changes of dN/dS within gene trees, and found that some coat protein gene trees have significantly different dN/dS between the B subtilis-clade and the B. cereus-clade.

Conclusions: Coat proteins in the B. subtilis- and B. cereus-group species are under contrasting selective pressures. We speculate that the absence of the exosporium in the B. subtilis spore coat effectively lifted a structural constraint that has led to relaxed negative selection pressure on the outer coat.

Show MeSH
Related in: MedlinePlus