Summary of orthologous relationships among the proteins deduced from all CDSs identified in the genomes of bacilli and other major Gram-positive species. (A) Orthologous relationships based on the O.iheyensis genome. (B) Orthologous relationships based on the B.halodurans genome. (C) Orthologous relationships based on the B.subtilis genome. OB, O.iheyensis; BH, B.halodurans; BS, B.subtilis; SA, S.aureus; CA, C.acetobutylicum.

Comparison of ortholog organization among the genomes of three Bacillus-related species. (A) In the case of 1803 orthologs identified in comparison with only three Bacillus-related species. (B) In the case of 354 orthologs identified in comparison with all five Gram-positive species (OB/BH/BS in Fig. 2). The dots are plotted at the positions where the gene for an orthologous protein exists when comparing two genomes. The scale of 360°, beginning with 0 at the dnaA locus (oriC), is based on the B.halodurans and B.subtilis maps. OB, O.iheyensis; BH, B.halodurans; BS, B.subtilis, SA, S.aureus; CA, C.acetobutylicum.

Circular representation of the alkaliphilic and extremely halotolerant O.iheyensis genome. (A) General view of the O.iheyensis HTE831 chromosome. The distribution of CDSs is depicted by colored boxes according to functional categories and direction of transcription (outer circle, plus strand; inner circle, minus strand; red, cell wall, sensors, motility and chemotaxis, protein secretion, cell division and transformation/competence; magenta, transport/binding proteins and lipoptoteins and membrane bioenergetics; gold, sporulation and germination; yellow/green, intermediary metabolism; gray, DNA replication, DNA restriction/modification and repair, DNA recombination and DNA packaging and segregation; pink, RNA synthesis; blue, protein synthesis; forest green, miscellaneous functions; sky blue, conserved CDSs with unknown function; coral, non-conserved proteins). The third and fourth circles indicate the distribution of rRNA and tRNA in the genome, respectively. (B) Distribution of orthologs identified among five genomes of major Gram-positive bacterial species based on the proteins deduced from the CDSs identified in the O.iheyensis genome. The distribution of orthologs is depicted by colored boxes (outermost circle, O.iheyensis; second circle, B.halodurans; third circle, B.subtilis; fourth circle, S.aureus; innermost circle, C.acetobutylicum). The blank spaces on the outermost circle indicate the location of RNA elements with no ortholog compared with the HTE831 genome in the case of the other circles. A linear map of the genes, with color codes for functional categories, is available at http://www.jamstec.go.jp/jamstec-e/bio/jp/topj.html.

Functional assignment of CDSs based on the orthologous relationships. (A) Orphans which have no orthologous relationship to four other Gram-positive species. (B) Orthologs identified among the genomes of five Gram-positive bacterial species. (D) Orthologs identified among the genomes of three Bacillus-related species. (C) Orthologs identified between O.iheyensis and B.halodurans, both alkaliphiles. The functional categories used at the B.subtilis genome database (SubtiList, http://www.pasteur.fr/Bio/SubtiList.html) were applied to this study. (C) Orthologs identified between O.iheyensis and B.halodurans, both alkaliphiles. (D) Orthologs identified among the genomes of three Bacillus-related species.

Overview of putative major transport systems that govern alkaliphily and extreme halotolerance in O.iheyensis. Overview of the cell wall system and the enzymes involved in the respiratory chain (yellow) are also shown. Transporters are grouped by their category: sodium cycle (blue), organic osmotic solutes such as glycine betaine, choline, carnitine, proline and pantothenate (green), carboxylic acids such as malate, fumarate and succinate (purple) and peptides and amino acids (red). ABC transport systems are shown as composite figures of oval, circular and sickle shape. The gene number of O.iheyensis corresponding to each component of the transporter is described below or above each figure. Atp, F₁F₀ ATP synthase; ABC, ABC transporter; BCCT, glycine betaine, carnitine/H⁺ symporter; Cba, cytochrome c oxidase (bo3-type); Cyd, cytochrome bd oxidase; I, NADH dehydrogenase; II, succinate dehydrogenase; III, menaquinol cytochrome c oxidoreductase; IV, cytochrome caa3 oxidase; Dct, C₄-dicarboxylate transport system; Mrp, Na⁺/H⁺ antiporter; Mot, channel for energization of motility; Nha, Na⁺/H⁺ antiporter; OPU, glycine betaine ABC transporter; PUT, proline/Na⁺ symporter and pantothenate/Na⁺ symporter; and Qox, cytochrome aa3 quinol oxidase; Sc, voltage-gated sodium channel.