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.

Branched fatty acids inhibit the biosynthesis of menaquinone in Helicobacter pylori

“…By genome sequencing, the latter strain was shown to be quite similar to the former strain in terms of genome size, G+C content of genomic DNA and the physiological properties used for taxonomical identification. 6 Moreover, the phylogenetic placement of B. halodurans C-125 based on 16S rDNA sequence analysis indicated that this organism is more closely related to B. subtilis than to other members of the genus Bacillus. 6 For example, both strains showed similar MIC values against representative antibiotics except for clarithromycin ( Table 1).…”

“…6 Moreover, the phylogenetic placement of B. halodurans C-125 based on 16S rDNA sequence analysis indicated that this organism is more closely related to B. subtilis than to other members of the genus Bacillus. 6 For example, both strains showed similar MIC values against representative antibiotics except for clarithromycin ( Table 1). The resistance to clarithromycin was probably caused by the presence of an ermD gene that encodes the ribosome-methylation enzyme in B. halodurans.…”

“…7 However, judging from the genome database of these strains, B. subtilis and B. halodurans C-125 use the classical pathway and the futalosine pathway, respectively, for the biosynthesis of MK. 6 These facts suggested that a compound inhibiting the biosynthesis of MK in the futalosine pathway specifically represses the growth of only B. halodurans C-12. Therefore, we first screened candidate compounds for their ability to specifically inhibit B. halodurans C-125 using a paper disk assay.…”

DNA Sequencing and Transcriptional Analysis of the Kasugamycin Biosynthetic Gene Cluster from Streptomyces kasugaensis M338-M1

“…The deduced amino acid sequence of KasN (383 amino acids, M r of 41,699, pI of 5.12) included a glycine box motif (GDGLIG) at positions 13ϳ18 that could allow binding of an FAD. Homology analysis of KasN showed similarity to D-amino acid oxidase (Protein ID: AAG07936.1) [11] from Pseudomonas aeruginosa (35% identity) and glycine oxidase (Protein ID: BAB05153.1) [12] from Bacillus halodurans (32% identity). In addition, KasN had some similarity to N-formimidoyl fortimicin A (FI-FTM A) synthase [13] from Micromonospora olivasterospora (31% identity).…”

Identification of tirandamycins as specific inhibitors of the futalosine pathway

“…By genome sequencing, these two strains had been shown to possess a high degree of similarity. 9 However, B. subtilis strain 168 and B.…”