Whole-genome phylogenies of the family Bacillaceae and expansion of the sigma factor gene family in the Bacillus cereus species-group

Abstract

Background: The Bacillus cereus sensu lato group consists of six species (B. anthracis, B. cereus, B. mycoides, B. pseudomycoides, B. thuringiensis, and B. weihenstephanensis). While classical microbial taxonomy proposed these organisms as distinct species, newer molecular phylogenies and comparative genome sequencing suggests that these organisms should be classified as a single species (thus, we will refer to these organisms collectively as the Bc species-group). How do we account for the underlying similarity of these phenotypically diverse microbes? It has been established for some time that the most rapidly evolving and evolutionarily flexible portions of the bacterial genome are regulatory sequences and transcriptional networks. Other studies have suggested that the sigma factor gene family of these organisms has diverged and expanded significantly relative to their ancestors; sigma factors are those portions of the bacterial transcriptional apparatus that control RNA polymerase recognition for promoter selection. Thus, examining sigma factor divergence in these organisms would concurrently examine both regulatory sequences and transcriptional networks important for divergence. We began this examination by comparison to the sigma factor gene set of B. subtilis.

Results: Phylogenetic analysis of the Bc species-group utilizing 157 single-copy genes of the family Bacillaceae suggests that several taxonomic revisions of the genus Bacillus should be considered. Within the Bc species-group there is little indication that the currently recognized species form related sub-groupings, suggesting that they are members of the same species. The sigma factor gene family encoded by the Bc species-group appears to be the result of a dynamic gene-duplication and gene-loss process that in previous analyses underestimated the true heterogeneity of the sigma factor content in the Bc species-group.

Conclusions: Expansion of the sigma factor gene family appears to have preferentially occurred within the extracytoplasmic function (ECF) sigma factor genes, while the primary alternative (PA) sigma factor genes are, in general, highly conserved with those found in B. subtilis. Divergence of the sigma-controlled transcriptional regulons among various members of the Bc species-group likely has a major role in explaining the diversity of phenotypic characteristics seen in members of the Bc species-group.

Figure 1

Whole genome single-copy gene phylogeny of the family Bacillaceae and the Bc species-group. Relationships among members of the family Bacillaceae based on the results obtained from a maximum-likelihood analysis of 157 single-copy genes found in each of the 43 genomes included in the analysis, using the genomes of Paenibacillus JDR-2 and Brevibacillus brevis NBRC-100599 to root the analysis. Numbers along the internodes are the number of times that node was supported in 100 bootstrap replicates. This is a phylogram that displays the relationships of all of the Bacillaceae; the legend denotes substitutions per nucleotide.

Figure 2

Whole-genome single-copy gene phylogeny of the Bc-species group. This analysis was performed as for Figure. 1, except that as the relationships between members of the Bc species-group were not resolved by this maximum iikelihood analysis (data not shown), Figure 2 is a cladogram that more clearly delineates the relationships within the Bc species-group.

Figure 3

Correlation of genome size with the number of PA and ECF sigma factors in Bacillaceae. The number of PA (black circles) and ECF (open circles) sigma factors genes identified in the genomes listed in Table 1 are plotted against genome size. The highlighted grey area is the observed number of PA and ECF sigma factor genes found for members of the Bc species-group. These results show that the number of ECF, but not PA, sigma factor genes is correlated with genome size.

Figure 4

Phylogenetic distribution of PA sigma factors in the Bc species-group. Sigma factors genes found in fewer than all of the genomes listed in Table 1, mapped on a Bc species-group cladeogram similar to that shown in Figure 2. The five Ba strains in Table 1 have a gene content identical to strain Ba strain Sterne, and so are condensed to one line in this tree. A + indicates the presence of a gene, as listed in the column heading, in that genome. Genome abbreviations are as found in Table 1.

Figure 5

Phylogenetic distribution of ECF sigma factors in the Bc species-group. Presentation and analyses are as described for Figure 4.