Limits...
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.

Show MeSH

Related in: MedlinePlus

The species reference tree of the Bacillus species under study based on 34 concatenated essential genes. The Newick format of this tree is (((Bpu,(Bli,(Bam,(Bmo,Bsu)))),(Bwe,(Bce,Ban,Bth))),(Bha,Bcl)). The evolutionary history was inferred using the neighbor-joining method. The optimal tree with the sum of branch length = 1.58 is shown. The percentages of replicate trees in which the associated taxa clustered together in the bootstrap test (1000 replicates) are shown next to the branches. The tree is drawn to scale, with branch lengths in the same units as those of the evolutionary distances used to infer the phylogenetic tree. The evolutionary distances were computed using the JTT matrix-based method and are in the units of the number of amino acid substitutions per site. All positions containing gaps and missing data were eliminated from the dataset. Phylogenetic analyses were conducted in MEGA4.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4219348&req=5

Figure 2: The species reference tree of the Bacillus species under study based on 34 concatenated essential genes. The Newick format of this tree is (((Bpu,(Bli,(Bam,(Bmo,Bsu)))),(Bwe,(Bce,Ban,Bth))),(Bha,Bcl)). The evolutionary history was inferred using the neighbor-joining method. The optimal tree with the sum of branch length = 1.58 is shown. The percentages of replicate trees in which the associated taxa clustered together in the bootstrap test (1000 replicates) are shown next to the branches. The tree is drawn to scale, with branch lengths in the same units as those of the evolutionary distances used to infer the phylogenetic tree. The evolutionary distances were computed using the JTT matrix-based method and are in the units of the number of amino acid substitutions per site. All positions containing gaps and missing data were eliminated from the dataset. Phylogenetic analyses were conducted in MEGA4.

Mentions: A defined species reference tree is important in phylogenetic analysis [43,44]. However, species trees of bacteria are difficult to construct [45]. The B. cereus sensu lato group is known to be very closely related. Sequence variations suggest that the B. cereus sensu lato group is a group of asexual clonal lineages [46]. B. cereus is also known to be an intermingled cluster of genetically diverse strains [47]. To facilitate appropriate molecular evolution analysis, we chose in this study to infer a species reference tree using only the fully sequenced genomes of species type strains. We used the concatenated sequences of 34 essential genes and generated a species reference (Figure 2), which is consistent with the 16S rRNA gene tree and previous reports (see Methods). Given that many bacterial gene trees may differ from the species reference tree, we tested alternative tree topologies and found that alternative branching patterns within the two major clades are mostly acceptable (see Methods).


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)

The species reference tree of the Bacillus species under study based on 34 concatenated essential genes. The Newick format of this tree is (((Bpu,(Bli,(Bam,(Bmo,Bsu)))),(Bwe,(Bce,Ban,Bth))),(Bha,Bcl)). The evolutionary history was inferred using the neighbor-joining method. The optimal tree with the sum of branch length = 1.58 is shown. The percentages of replicate trees in which the associated taxa clustered together in the bootstrap test (1000 replicates) are shown next to the branches. The tree is drawn to scale, with branch lengths in the same units as those of the evolutionary distances used to infer the phylogenetic tree. The evolutionary distances were computed using the JTT matrix-based method and are in the units of the number of amino acid substitutions per site. All positions containing gaps and missing data were eliminated from the dataset. Phylogenetic analyses were conducted in MEGA4.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 2: The species reference tree of the Bacillus species under study based on 34 concatenated essential genes. The Newick format of this tree is (((Bpu,(Bli,(Bam,(Bmo,Bsu)))),(Bwe,(Bce,Ban,Bth))),(Bha,Bcl)). The evolutionary history was inferred using the neighbor-joining method. The optimal tree with the sum of branch length = 1.58 is shown. The percentages of replicate trees in which the associated taxa clustered together in the bootstrap test (1000 replicates) are shown next to the branches. The tree is drawn to scale, with branch lengths in the same units as those of the evolutionary distances used to infer the phylogenetic tree. The evolutionary distances were computed using the JTT matrix-based method and are in the units of the number of amino acid substitutions per site. All positions containing gaps and missing data were eliminated from the dataset. Phylogenetic analyses were conducted in MEGA4.
Mentions: A defined species reference tree is important in phylogenetic analysis [43,44]. However, species trees of bacteria are difficult to construct [45]. The B. cereus sensu lato group is known to be very closely related. Sequence variations suggest that the B. cereus sensu lato group is a group of asexual clonal lineages [46]. B. cereus is also known to be an intermingled cluster of genetically diverse strains [47]. To facilitate appropriate molecular evolution analysis, we chose in this study to infer a species reference tree using only the fully sequenced genomes of species type strains. We used the concatenated sequences of 34 essential genes and generated a species reference (Figure 2), which is consistent with the 16S rRNA gene tree and previous reports (see Methods). Given that many bacterial gene trees may differ from the species reference tree, we tested alternative tree topologies and found that alternative branching patterns within the two major clades are mostly acceptable (see Methods).

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