Genome Sequence of Bacillus licheniformis WX-02

Abstract

Bacillus licheniformis is an important bacterium that has been used extensively for large-scale industrial production of exoenzymes and peptide antibiotics. B. licheniformis WX-02 produces poly-gamma-glutamate increasingly when fermented under stress conditions. Here its genome sequence (4,270,104 bp, with G+C content of 46.06%), which comprises a circular chromosome, is announced.

GENOME ANNOUNCEMENT

Bacillus licheniformis is a Gram-positive bacterium which inhabits soil and readily forms endospores. Agriculturally, it has been used as a probiotic and microbial fertilizer (9); industrially, it is used to produce enzymatic agents (12), peptide antibiotics (7), acetoin (8), and poly-γ-glutamic acid (γ-PGA) (1, 2), etc. B. licheniformis WX-02 was isolated from saline soil in Yingcheng City, Hubei Province, China. It has been noted that this strain can produce larger amounts of γ-PGA under stress conditions than under normal ones; the stresses refer to high salt, high temperature, caustic alkali, ultrasonic shock, and so on. The yield of γ-PGA can be raised 5.28 times against that of the control group when the salt concentration reaches 8% (13). In order to explore the mechanism of high production of γ-PGA under adverse circumstances, the genome of B. licheniformis WX-02 was sequenced and compared with that of the type strain ATCC 14580 (10, 12). B. licheniformis WX-02 has been maintained at the China Center for Type Culture Collection and designated B. licheniformis CCTCC M208065.

Whole-genome sequencing was performed using a Solexa genome analyzer (BGI; Shenzhen, China) using a shotgun strategy, which produced paired reads totaling ∼555 Mb with about 131-fold coverage of the genome. Genome sequence data were processed and assembled into 45 contigs and 29 scaffolds (5). Gaps between contigs were closed by combinatorial PCR and sequencing amplicons by primer walking. Finally, this assembling process produced 3 large scaffolds in one potential circular chromosome. Open reading frames were identified using Fgenesb (http://linux1.softberry.com/berry.phtml?topic=fgenesb&group=programs&subgroup=gfindb), Prodigal (http://compbio.ornl.gov/prodigal/), and Glimmer (http://www.ncbi.nlm.nih.gov/genomes/MICROBES/glimmer_3.cgi) and BLAST against the RefSeq database. tRNA and rRNA genes were identified by the tRNAScan and RNAmmer software programs, respectively (4, 6). The genome of strain CCTCC M208065 is 4,270,104 bp long with a GC content of 46.06%, containing 4,320 open reading frames, 72 tRNA genes, and 7 rRNA operons. Although the genome of CCTCC M208065 shares great similarity (94.8%) with that of ATCC 14580, genome comparison indicates that two large (more than 50 kb) fragments are translocated in CCTCC M208065, which extends our understanding of genome evolution. In addition, there is a fragment of about 76 kb in this genome sharing very low homology with the genome of ATCC 14580 and other sequences in GenBank; this fragment encodes the DNA replication initiator protein, conjugation protein, RNA polymerase sigma factors, transcriptional regulators, recombinases, hypothetical proteins, and others.

It has been reported that the gene cluster comQXPA is involved in regulation of γ-PGA synthesis (3, 11). The comP gene in the ATCC 14580 strain is inactivated by two insertional fragments, while this gene in CCTCC M208065 is complete. The difference in the comP gene between these two strains might be associated with their different abilities for γ-PGA production, although much evidence is needed to verify this.

Nucleotide sequence accession numbers.

This whole-genome shotgun project has been deposited in DDBJ/EMBL/GenBank under the accession no. AHIF00000000. The version described in this paper is the first version, AHIF01000000.