Complete genome sequence of the alkaliphilic bacterium Bacillus halodurans and genomic sequence comparison with Bacillus subtilis

Abstract

The 4 202 353 bp genome of the alkaliphilic bacterium Bacillus halodurans C-125 contains 4066 predicted protein coding sequences (CDSs), 2141 (52.7%) of which have functional assignments, 1182 (29%) of which are conserved CDSs with unknown function and 743 (18. 3%) of which have no match to any protein database. Among the total CDSs, 8.8% match sequences of proteins found only in Bacillus subtilis and 66.7% are widely conserved in comparison with the proteins of various organisms, including B.subtilis. The B. halodurans genome contains 112 transposase genes, indicating that transposases have played an important evolutionary role in horizontal gene transfer and also in internal genetic rearrangement in the genome. Strain C-125 lacks some of the necessary genes for competence, such as comS, srfA and rapC, supporting the fact that competence has not been demonstrated experimentally in C-125. There is no paralog of tupA, encoding teichuronopeptide, which contributes to alkaliphily, in the C-125 genome and an ortholog of tupA cannot be found in the B.subtilis genome. Out of 11 sigma factors which belong to the extracytoplasmic function family, 10 are unique to B. halodurans, suggesting that they may have a role in the special mechanism of adaptation to an alkaline environment.

Figure 1

General view of the alkaliphilic B.halodurans C-125 chromosome. Arrows indicate the direction of transcription. Genes are colored according to their classification into nine broad categories (green, protein conserved in comparison with other organisms, including B.subtilis; striped green, unknown; red, protein conserved in comparison with organisms other than B.subtilis; striped red, protein conserved in comparison with organisms other than members of Bacillus; striped yellow, protein conserved in comparison with other members of Bacillus, including B.subtilis; striped blue, protein conserved in comparison only with B.subtilis; striped pink, protein related to alkaliphily in C-125; purple, protein conserved in comparison with members of Bacillus other than B.subtilis; see Table S1). Ribosomal RNA genes are colored purple and shown as thin arrows. tRNA genes are marked as vertical bars on the line.

Figure 1

General view of the alkaliphilic B.halodurans C-125 chromosome. Arrows indicate the direction of transcription. Genes are colored according to their classification into nine broad categories (green, protein conserved in comparison with other organisms, including B.subtilis; striped green, unknown; red, protein conserved in comparison with organisms other than B.subtilis; striped red, protein conserved in comparison with organisms other than members of Bacillus; striped yellow, protein conserved in comparison with other members of Bacillus, including B.subtilis; striped blue, protein conserved in comparison only with B.subtilis; striped pink, protein related to alkaliphily in C-125; purple, protein conserved in comparison with members of Bacillus other than B.subtilis; see Table S1). Ribosomal RNA genes are colored purple and shown as thin arrows. tRNA genes are marked as vertical bars on the line.

Figure 1

General view of the alkaliphilic B.halodurans C-125 chromosome. Arrows indicate the direction of transcription. Genes are colored according to their classification into nine broad categories (green, protein conserved in comparison with other organisms, including B.subtilis; striped green, unknown; red, protein conserved in comparison with organisms other than B.subtilis; striped red, protein conserved in comparison with organisms other than members of Bacillus; striped yellow, protein conserved in comparison with other members of Bacillus, including B.subtilis; striped blue, protein conserved in comparison only with B.subtilis; striped pink, protein related to alkaliphily in C-125; purple, protein conserved in comparison with members of Bacillus other than B.subtilis; see Table S1). Ribosomal RNA genes are colored purple and shown as thin arrows. tRNA genes are marked as vertical bars on the line.

Figure 1

General view of the alkaliphilic B.halodurans C-125 chromosome. Arrows indicate the direction of transcription. Genes are colored according to their classification into nine broad categories (green, protein conserved in comparison with other organisms, including B.subtilis; striped green, unknown; red, protein conserved in comparison with organisms other than B.subtilis; striped red, protein conserved in comparison with organisms other than members of Bacillus; striped yellow, protein conserved in comparison with other members of Bacillus, including B.subtilis; striped blue, protein conserved in comparison only with B.subtilis; striped pink, protein related to alkaliphily in C-125; purple, protein conserved in comparison with members of Bacillus other than B.subtilis; see Table S1). Ribosomal RNA genes are colored purple and shown as thin arrows. tRNA genes are marked as vertical bars on the line.

Figure 1

General view of the alkaliphilic B.halodurans C-125 chromosome. Arrows indicate the direction of transcription. Genes are colored according to their classification into nine broad categories (green, protein conserved in comparison with other organisms, including B.subtilis; striped green, unknown; red, protein conserved in comparison with organisms other than B.subtilis; striped red, protein conserved in comparison with organisms other than members of Bacillus; striped yellow, protein conserved in comparison with other members of Bacillus, including B.subtilis; striped blue, protein conserved in comparison only with B.subtilis; striped pink, protein related to alkaliphily in C-125; purple, protein conserved in comparison with members of Bacillus other than B.subtilis; see Table S1). Ribosomal RNA genes are colored purple and shown as thin arrows. tRNA genes are marked as vertical bars on the line.

Figure 1

General view of the alkaliphilic B.halodurans C-125 chromosome. Arrows indicate the direction of transcription. Genes are colored according to their classification into nine broad categories (green, protein conserved in comparison with other organisms, including B.subtilis; striped green, unknown; red, protein conserved in comparison with organisms other than B.subtilis; striped red, protein conserved in comparison with organisms other than members of Bacillus; striped yellow, protein conserved in comparison with other members of Bacillus, including B.subtilis; striped blue, protein conserved in comparison only with B.subtilis; striped pink, protein related to alkaliphily in C-125; purple, protein conserved in comparison with members of Bacillus other than B.subtilis; see Table S1). Ribosomal RNA genes are colored purple and shown as thin arrows. tRNA genes are marked as vertical bars on the line.

Figure 1

General view of the alkaliphilic B.halodurans C-125 chromosome. Arrows indicate the direction of transcription. Genes are colored according to their classification into nine broad categories (green, protein conserved in comparison with other organisms, including B.subtilis; striped green, unknown; red, protein conserved in comparison with organisms other than B.subtilis; striped red, protein conserved in comparison with organisms other than members of Bacillus; striped yellow, protein conserved in comparison with other members of Bacillus, including B.subtilis; striped blue, protein conserved in comparison only with B.subtilis; striped pink, protein related to alkaliphily in C-125; purple, protein conserved in comparison with members of Bacillus other than B.subtilis; see Table S1). Ribosomal RNA genes are colored purple and shown as thin arrows. tRNA genes are marked as vertical bars on the line.

Figure 1

General view of the alkaliphilic B.halodurans C-125 chromosome. Arrows indicate the direction of transcription. Genes are colored according to their classification into nine broad categories (green, protein conserved in comparison with other organisms, including B.subtilis; striped green, unknown; red, protein conserved in comparison with organisms other than B.subtilis; striped red, protein conserved in comparison with organisms other than members of Bacillus; striped yellow, protein conserved in comparison with other members of Bacillus, including B.subtilis; striped blue, protein conserved in comparison only with B.subtilis; striped pink, protein related to alkaliphily in C-125; purple, protein conserved in comparison with members of Bacillus other than B.subtilis; see Table S1). Ribosomal RNA genes are colored purple and shown as thin arrows. tRNA genes are marked as vertical bars on the line.

Figure 2

Comparison of G+C profile between the genomes of B.halodurans and B.subtilis. Distribution of A+T-rich islands along the chromosome, in sliding windows of 10 000 nt, with a step of 5000 nt. Known phage (PBSX, SPβ and skin) are indicated by their names and prophage-like elements in the B.subtilis genome are numbered from P1 to P7. The A+T-rich or G+C-rich regions containing transposases in the B.halodurans genome are also indicated from T1 to T11. (A) B.subtilis; (B) B.halodurans.

Figure 3

Summary of conserved CDSs identified in the genome of B.halodurans C-125. (A) All CDSs; (B) CDSs with a known functional role; (C) CDSs of unknown function

Figure 4

Structural analysis of the B.halodurans and B.subtilis genomes. (A) Distribution of regions having a nucleotide sequence common to the two Bacillus spp. The dots were plotted when more than 20 bases of the nucleotide sequence matched continuously with that of B.subtilis in a sliding window 100 nt wide with a step of 50 nt. The columns appearing as a bar code clearly show the regions shared between the B.halodurans and B.subtilis genomes. (B) Distribution of orthologs between the two Bacillus spp. The dots were plotted at the positions where the gene for an orthologous protein exists when comparing the two genomes. The columns appearing as a bar code clearly show the positions of the genes for orthologous proteins in B.halodurans and B.subtilis.