Distribution of interspersed DNA repeats of 100 bp or more in the chromosome of B. pseudofirmus OF4. Each repeat element (bpr1, bpr2 and bcr3) is drawn in a different color. Repeat copies are numbered consecutively. Copies located on the forward DNA strand are drawn above the thick grey line representing the chromosome and their names contain the letter F, whereas copies located on the reverse strand are drawn below the grey line and their names contain the letter R. Partial copies of the bpr2 repeat element are indicated with names starting with the letter P. The figure was generated using CGview (Stothard & Wishart, 2005).

Predicted amino acid sequences from 7 complete Bacillus genomes were submitted to the Compute pI / Mw Tool at the Swiss Institute of Bioinformatics ExPASy Proteomics Server (http://ca.expasy.org/tools/pi_tool.html). The same sequences were also submitted to PSORTb v3.0 (Yu et al., 2010) for determination of subcellular location. Comparison of the means between B. pseudofirmus OF4 and the six other Bacilli was performed with unpaired 2-sample T-tests. ** p<0.0001, * p<0.05

Features of the Bacillus pseudofirmus OF4 genome that are proposed adaptations to the energy demands and overlapping stresses related to alkaliphily and reveal structural and metabolic properties not found in closely related Bacillus halodurans C-125. The selected metabolic pathways shown focus on energy-generation and potential stored energy forms (light blue). Dashed arrows represent multi-step pathways for which only representative enzymes are shown. The primary transporter groups (shown in aqua) are predicted to have roles in antibiotic resistance/cell envelope stress, nutrient uptake, and ion homeostasis. The ABC-type MDRs (multi-drug transporters) included in the 36 total MDRs are also counted in the ABC transporter total of 49. The selected groups of secondary transporters that are shown have potential or established roles in: cytoplasmic pH homeostasis (yellow); sodium-dependent efflux of toxins and uptake of nutrients, ions or compatible solutes (gray); and the TRAP-T transporters, with DCA (dicarboxylic acids as a substrate), whcih are highlighted in purple because the 24 loci significantly exceeds the 16 loci found in the B. halodurans C-125 genome. See text for full names of transporters abbreviated here. The representative channels (green) that are shown have roles in motility, pH homeostasis, osmo-regulation, cation and nutrient uptake. In the square-shaped figure that represents a rod-shaped bacterium, the top/bottom represent the long sides, where the flagellum is found, and the sides represent the poles, where the sodium channel and chemotaxis receptors and unreleased spores are localized. The other localizations are not known. Outside bottom left corner: peptidoglycan and additional cell wall associated polymers and proteins are shown. Examples of elements not found in Bacillus halodurans C-125 (highlighted or outlined in purple) are: two of the putative energy storage forms, polyhydroxyalkanoates and polyglutamate capsule; cell wall S-layer and SLH-domain proteins; cell membrane triterpenoid carotenoid; gas vacuoles; a NiFe hydrogenase/cytochrome b5 locus; enzymes and regulators of polyaromatic hydrocarbon metabolism; and a malonate utilization locus.

Circular representation of the B. pseudofirmus OF4 genome. Black arrow – dnaA gene (oriC). Blue bars – genes on the forward strand, red bars – genes on the reverse strand, green bars – ribosomal RNA, black bars – tRNAs. Black ring – GC plot, Orange and blue ring – GC skew.