PMID:19285085

Citation	Stewart, CR, Casjens, SR, Cresawn, SG, Houtz, JM, Smith, AL, Ford, ME, Peebles, CL, Hatfull, GF, Hendrix, RW, Huang, WM and Pedulla, ML (2009) The genome of Bacillus subtilis bacteriophage SPO1. J. Mol. Biol. 388:48-70
Abstract	We report the genome sequence of Bacillus subtilis phage SPO1. The unique genome sequence is 132,562 bp long, and DNA packaged in the virion (the chromosome) has a 13,185-bp terminal redundancy, giving a total of 145,747 bp. We predict 204 protein-coding genes and 5 tRNA genes, and we correlate these findings with the extensive body of investigations of SPO1, including studies of the functions of the 61 previously defined genes and studies of the virion structure. Sixty-nine percent of the encoded proteins show no similarity to any previously known protein. We identify 107 probable transcription promoters; most are members of the promoter classes identified in earlier studies, but we also see a new class that has the same sequence as the host sigma K promoters. We find three genes encoding potential new transcription factors, one of which is a distant homologue of the host sigma factor K. We also identify 75 probable transcription terminator structures. Promoters and terminators are generally located between genes and together with earlier data give what appears to be a rather complete picture of how phage transcription is regulated. There are complete genome sequences available for five additional phages of Gram-positive hosts that are similar to SPO1 in genome size and in composition and organization of genes. Comparative analysis of SPO1 in the context of these other phages yields insights about SPO1 and the other phages that would not be apparent from the analysis of any one phage alone. These include assigning identities as well as probable functions for several specific genes and inferring evolutionary events in the phages' histories. The comparative analysis also allows us to put SPO1 into a phylogenetic context. We see a pattern similar to what has been noted in phage T4 and its relatives, in which there is minimal successful horizontal exchange of genes among a "core" set of genes that includes most of the virion structural genes and some genes of DNA metabolism, but there is extensive horizontal transfer of genes over the remainder of the genome. There is a correlation between genes in rapid evolutionary flux through these genomes and genes that are small.
Links	PubMed PMC2666789 Online version:10.1016/j.jmb.2009.03.009
Keywords	Bacillus Phages/genetics; Bacillus subtilis/virology; Base Sequence; Binding Sites; DNA, Viral/chemistry; Evolution, Molecular; Genome, Viral; Molecular Sequence Data; Open Reading Frames; Viral Proteins/genetics
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Annotations

Gene product	Qualifier	GO Term	Evidence Code	with/from	Aspect	Extension	Notes	Status
BPSP1:PORTL		GO:0046798: viral portal complex	ECO:0000317:	UniProtKB:B6V2N5 UniProtKB:Q4Z9G3	C		Fig 3. shows synteny between the portal protein of SPO1 and phages, LP65, Twort, P100, and K/G. In all phages, the portal protein is located "immediately upstreams of the procapsid protease gene" or Gp3.2 (B6V2N5).	complete CACAO 11848
BPSP1:B6V2P5		GO:0098026: virus tail, tube	IGC: Inferred from Genomic Context: UniProtKB:B6V2P4	C	In this paper, specifically in the section about tail assembly proteins, the authors discuss the potential function of gene 10.1. They speculate it might be a tail tube protein because the length of gene 10.1 corresponds to a gene that codes for a tail tube protein. Additionally, figure 5 shows how the authors analyzed other homologs to show how 10.01 was a tail tube protein.	complete CACAO 11763

References

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