Complete genome sequence of the industrial bacterium Bacillus licheniformis and comparisons with closely related Bacillus species

Genome Biology, Sep 2004

Background Bacillus licheniformis is a Gram-positive, spore-forming soil bacterium that is used in the biotechnology industry to manufacture enzymes, antibiotics, biochemicals and consumer products. This species is closely related to the well studied model organism Bacillus subtilis, and produces an assortment of extracellular enzymes that may contribute to nutrient cycling in nature. Results We determined the complete nucleotide sequence of the B. licheniformis ATCC 14580 genome which comprises a circular chromosome of 4,222,336 base-pairs (bp) containing 4,208 predicted protein-coding genes with an average size of 873 bp, seven rRNA operons, and 72 tRNA genes. The B. licheniformis chromosome contains large regions that are colinear with the genomes of B. subtilis and Bacillus halodurans, and approximately 80% of the predicted B. licheniformis coding sequences have B. subtilis orthologs. Conclusions Despite the unmistakable organizational similarities between the B. licheniformis and B. subtilis genomes, there are notable differences in the numbers and locations of prophages, transposable elements and a number of extracellular enzymes and secondary metabolic pathway operons that distinguish these species. Differences include a region of more than 80 kilobases (kb) that comprises a cluster of polyketide synthase genes and a second operon of 38 kb encoding plipastatin synthase enzymes that are absent in the B. licheniformis genome. The availability of a completed genome sequence for B. licheniformis should facilitate the design and construction of improved industrial strains and allow for comparative genomics and evolutionary studies within this group of Bacillaceae.

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Complete genome sequence of the industrial bacterium Bacillus licheniformis and comparisons with closely related Bacillus species

Genome Biology Re e2VRt0oea0yluls4.meea5r,cIshsue 10, Article R77 Complete genome sequence of the industrial bacterium Bacillus licheniformis and comparisons with closely related Bacillus species Michael W Rey 2 Preethi Ramaiya 2 Beth A Nelson 2 Shari D Brody-Karpin 2 Elizabeth J Zaretsky 2 Maria Tang 2 Alfredo Lopez de Leon 2 Henry Xiang 2 Veronica Gusti 2 Ib Groth Clausen 0 4 Peter B Olsen 0 Michael D Rasmussen 0 Jens T Andersen 0 Per L Jrgensen 0 Thomas S Larsen 0 Alexei Sorokin 1 Alexander Bolotin 1 Alla Lapidus 1 3 Nathalie Galleron 1 S Dusko Ehrlich 1 Randy M Berka 2 0 Novozymes A/S , Bagsvaerd, DK-2880 , Denmark 1 Institut National de la Recherche Agronomique , Paris Cedex 75007 , France 2 Novozymes Biotech Inc , 1445 Drew Ave, Davis, CA 95616 , USA 3 Joint Genome Institute , Walnut Creek, CA 94598 , USA 4 AstraZeneca International , Lund SE221 87 , Sweden Background: Bacillus licheniformis is a Gram-positive, spore-forming soil bacterium that is used in the biotechnology industry to manufacture enzymes, antibiotics, biochemicals and consumer products. This species is closely related to the well studied model organism Bacillus subtilis, and produces an assortment of extracellular enzymes that may contribute to nutrient cycling in nature. Results: We determined the complete nucleotide sequence of the B. licheniformis ATCC 14580 genome which comprises a circular chromosome of 4,222,336 base-pairs (bp) containing 4,208 predicted protein-coding genes with an average size of 873 bp, seven rRNA operons, and 72 tRNA genes. The B. licheniformis chromosome contains large regions that are colinear with the genomes of B. subtilis and Bacillus halodurans, and approximately 80% of the predicted B. licheniformis coding sequences have B. subtilis orthologs. Conclusions: Despite the unmistakable organizational similarities between the B. licheniformis and B. subtilis genomes, there are notable differences in the numbers and locations of prophages, transposable elements and a number of extracellular enzymes and secondary metabolic pathway operons that distinguish these species. Differences include a region of more than 80 kilobases (kb) that comprises a cluster of polyketide synthase genes and a second operon of 38 kb encoding plipastatin synthase enzymes that are absent in the B. licheniformis genome. The availability of a completed genome sequence for B. licheniformis should facilitate the design and construction of improved industrial strains and allow for comparative genomics and evolutionary studies within this group of Bacillaceae. - Background Bacillus licheniformis is a Gram-positive, spore-forming bacterium widely distributed as a saprophytic organism in the environment. This species is a close relative of Bacillus subtilis, an organism that is second only to Escherichia coli in the level of detail at which it has been studied. Unlike most other bacilli, which are predominantly aerobic, B. licheniformis is a facultative anaerobe, which may allow it to grow in additional ecological niches. Certain B. licheniformis isolates are capable of denitrification; the relevance of this characteristic to environmental denitrification may be small, however, as the species generally persists in soil as endospores [1]. There are numerous commercial and agricultural uses for B. licheniformis and its extracellular products. The species has been used for decades in the manufacture of industrial enzymes including several proteases, -amylase, penicillinase, pentosanase, cycloglucosyltransferase, -mannanase and several pectinolytic enzymes. The proteases from B. licheniformis are used in the detergent industry as well as for dehairing and bating of leather [2,3]. Amylases from B. licheniformis are deployed for the hydrolysis of starch, desizing of textiles and sizing of paper [3]. Specific B. licheniformis strains are also used to produce peptide antibiotics such as bacitracin and proticin in addition to a number of specialty chemicals such as citric acid, inosine, inosinic acid and poly-glutamic acid [4]. Some B. licheniformis isolates can mitigate the affects of fungal pathogens on maize, grasses and vegetable crops [5]. As an endospore-forming bacterium, the ability of the organism to survive under unfavorable environmental conditions may enhance its potential as a natural biocontrol agent. B. licheniformis can be differentiated from other bacilli on the basis of metabolic and physiological tests [6,7]; however, biochemical and phenotypic characteristics may be ambiguous among closely related species. Recent taxonomic studies indicate that B. licheniformis is closely related to B. subtilis and Bacillus amyloliquefaciens on the basis of comparisons of 16S rDNA and 16S-23S internal transcribed spacer (ITS) nucleotide sequences [8]. Lapidus et al. [9] recently constructed a physical map of the B. licheniformis chromosome using a PCR approach, and established a number of regions of colinearity where gene content and organiz (...truncated)


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Michael W Rey, Preethi Ramaiya, Beth A Nelson, Shari D Brody-Karpin, Elizabeth J Zaretsky, Maria Tang, Alfredo de Leon, Henry Xiang, Veronica Gusti, Ib Groth Clausen, Peter B Olsen, Michael D Rasmussen, Jens T Andersen, Per L Jørgensen, Thomas S Larsen, Alexei Sorokin, Alexander Bolotin, Alla Lapidus, Nathalie Galleron, S Dusko Ehrlich, Randy M Berka. Complete genome sequence of the industrial bacterium Bacillus licheniformis and comparisons with closely related Bacillus species, Genome Biology, 2004, pp. r77, 5, DOI: 10.1186/gb-2004-5-10-r77