The Bacillus anthracis chromosome contains four conserved, excision-proficient, putative prophages

More than 300 geographically and temporally divergent isolates of B. anthracis and its near neighbors were screened by PCR for the presence of specific DNA sequences from each prophage region. Every isolate of B. anthracis screened by PCR was found to produce all four phage-specific amplicons whereas none of the non-B. anthracis isolates, produced more than one phage-specific amplicon. Excision of prophages could be detected by a PCR based assay for attP sites on extra-chromosomal phage circles and for attB sites on phage-excised chromosomes. SYBR-green real-time PCR assays indicated that prophage excision occurs at very low frequencies (2 × 10-5 - 8 × 10-8/cell). Induction with mitomycin C increased the frequency of excision of one of the prophages by approximately 250 fold. All four prophages appear to be defective since, mitomycin C induced culture did not release any viable phage particle or lyse the cells or reveal any phage particle under electron microscopic examination.The retention of all four putative prophage regions across all tested strains of B. anthracis is further evidence of the very recent emergence of this lineage and the prophage regions may be useful for differentiating the B. anthracis chromosome from that of its neighbors. All four prophages can excise at low frequencies, but are apparently defective in phage production.The genome sequence of the bioterrorism pathogen, Bacillus anthracis Ames strain, revealed the presence of four putative lambdoid prophages (designated lambdaBa0l, lambdaBa02, lambdaBa03 and lambdaBa04), constituting about 3% of the 5.2 Mbase main chromosome [1]. Comparative genomic hybridization studies showed that the prophage regions made up a higher percentage of the unique genes in B. anthracis not found in 19 other Bacillus cereus group strains [1]. DNA sequences of all completed and shotgun genome sequences of the diverse B. anthracis strains submitted to genbank (Genbank IDs: AE016879, AE017334, AAAC01000001, AAEQ000000