Abstract
A complete 39,318-bp genome sequence containing 52 coding sequences has been determined for the Bacillus subtilis temperate phage φ105. In a lysogen, B. subtilis strain 1L32, the φ105 prophage interrupts the radC locus, a part of the competence-induced ComK regulon.
GENOME ANNOUNCEMENT
Bacteriophage φ105, a well-studied temperate phage of Bacillus subtilis (1, 2), is capable of specialized transduction and has been developed into a system for cloning and expressing genes in this host (3, 4). Here I describe the complete genome resequencing of φ105.
The approximate chromosomal integration site for φ105 has been previously determined by hybridization studies (5). Genomic DNA from a B. subtilis φ105 lysogen, BGSC strain number 1L32, was sequenced in its prophage region by a primer-walking strategy. A total of 435 overlapping PCR fragments were sequenced at the Plant-Microbe Genomics Facility at the Ohio State University on an Applied Biosystems 3730 DNA analyzer using BigDye terminator cycle sequencing chemistry. Average coverage was 9.3×.
The φ105 genome is a linear 39,318-bp double-stranded DNA molecule capable of circularizing through 7-bp cohesive ends. There are 52 predicted coding sequences (CDS). The present sequence differs in 68 nucleotides (nt) from an unpublished genome sequence in the database (AB016282), correcting 15 probable frameshift errors in the older sequence and locating the phage attachment site for the first time. The φ105 prophage interrupts the radC gene in the B. subtilis 1L32 genome at a 10-bp attachment site (TGTTTATACTT). The radC gene is known to be transcriptionally activated by the master regulator of competence development in B. subtilis, ComK (6, 7). This observation may explain the so-called “naïve” phenotype of φ105: the prophage is induced not only by DNA-damaging agents, but also by competence development (8).
Nucleotide sequence accession numbers.
The complete genome sequence is deposited in GenBank under the accession no. HM072038. The version described in this paper is the first version, HM072038.1.
ACKNOWLEDGMENT
The Bacillus Genetic Stock Center is supported in part by a grant from the National Science Foundation (0234214).
Footnotes
Citation Ziegler DR. 2013. Complete genome sequence of Bacillus subtilis phage φ105. Genome Announc. 1(5):e00641-13. doi:10.1128/genomeA.00641-13.
REFERENCES
- 1. Birdsell DC, Hathaway GM, Rutberg L. 1969. Characterization of temperate Bacillus bacteriophage φ105. J. Virol. 4:264–270 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 2. Hemphill HE, Whiteley HR. 1975. Bacteriophages of Bacillus subtilis. Bacteriol. Rev. 39:257–315 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 3. Chan AY, Chan MM, Lo HM, Leung YC, Lim BL. 2002. A dual protein expression system in Bacillus subtilis. Protein Expr. Purif. 26:337–342 [DOI] [PubMed] [Google Scholar]
- 4. Errington J. 1984. Efficient Bacillus subtilis cloning system using bacteriophage vector φ105J9. J. Gen. Microbiol. 130:2615–2628 [DOI] [PubMed] [Google Scholar]
- 5. Levin PA, Margolis PS, Setlow P, Losick R, Sun D. 1992. Identification of Bacillus subtilis genes for septum placement and shape determination. J. Bacteriol. 174:6717–6728 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 6. Berka RM, Hahn J, Albano M, Draskovic I, Persuh M, Cui X, Sloma A, Widner W, Dubnau D. 2002. Microarray analysis of the Bacillus subtilis K-state: genome-wide expression changes dependent on ComK. Mol. Microbiol. 43:1331–1345 [DOI] [PubMed] [Google Scholar]
- 7. Ogura M, Yamaguchi H, Kobayashi K, Ogasawara N, Fujita Y, Tanaka T. 2002. Whole-genome analysis of genes regulated by the Bacillus subtilis competence transcription factor ComK. J. Bacteriol. 184:2344–2351 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 8. McVeigh RR, Yasbin RE. 1996. Phenotypic differentiation of “smart” versus “naive” bacteriophages of Bacillus subtilis. J. Bacteriol. 178:3399–3401 [DOI] [PMC free article] [PubMed] [Google Scholar]