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

Michael W Rey1, Preethi Ramaiya1, Beth A Nelson1, Shari D Brody-Karpin1, Elizabeth J Zaretsky1, Maria Tang1, Alfredo Lopez de Leon1, Henry Xiang1, Veronica Gusti1, Ib Groth Clausen24, Peter B Olsen2, Michael D Rasmussen2, Jens T Andersen2, Per L Jørgensen2, Thomas S Larsen2, Alexei Sorokin3, Alexander Bolotin3, Alla Lapidus35, Nathalie Galleron3, S Dusko Ehrlich3 and Randy M Berka1*

Author Affiliations

1 Novozymes Biotech Inc, 1445 Drew Ave, Davis, CA 95616, USA

2 Novozymes A/S, Bagsværd, DK-2880, Denmark

3 Institut National de la Recherche Agronomique, Paris Cedex 75007, France

4 AstraZeneca International, Lund SE221 87, Sweden

5 Joint Genome Institute, Walnut Creek, CA 94598, USA

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Genome Biology 2004, 5:r77  doi:10.1186/gb-2004-5-10-r77

Published: 13 September 2004

Abstract

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.