Physical map of bacteriophage BF23 DNA: terminal redundancy and localization of single-chain interruptions

Abstract

The DNA of bacteriophage BF23 possesses two structural features, localized single-chain interruptions and a large terminal repetition, previously described for T5, a closely related virus. As is the case for T5, single-chain interruptions occur with variable frequencies at a small number of fixed sites within one strand of the double-stranded BF23 genome. The sites where interruptions occur with the highest frequencies were mapped by an electrophoretic analysis of the singlestranded fragments produced by denaturation of BF23 DNA. The positions of these fragments were determined by degrading BF23 DNA to various extents with A exonuclease and observing the relative order with which they were (i) degraded or (ii) released intact from the undenatured duplex. The exact locations of the interruptions were determined from analysis of analogous duplex fragments produced by degrading exonuclease Ill-treated BF23 DNA with a single-strandspecific endonuclease. BF23 has five principal sites (located at 7.9, 18.7, 32.4, 65.8, and 99.6% from the left end of the DNA) where interruptions occur in most molecules. The principal interruptions in T5 DNA occur at similar positions. The locations of eight secondary interruptions in BF23 DNA were also determined. In general, BF23 DNA has fewer secondary interruptions than T5 DNA, although there is at least one location where an interruption occurs with a greater frequency in BF23. The presence bf a terminal repetition in BF23 DNA was demonstrated by annealing ligase-repaired molecules that had been partially digested with A exonuclease. If the complementary sequences at both ends of the DNA were exposed by exonuclease treatment, the duplex segment that resulted from annealing could be released by digestion with a single-strand-specific endonuclease. This segment was analyzed by agarose gel electrophoresis and found to represent 8.4% of BF23 DNA. nated BF23st(+), were obtained from J. Mc-Corquodale and G. Hayward. Two heat-stable deletion mutants, BF23st(102) and BF23st(104), were isolated 777

Discovery of Three Toxic Proteins of Klebsiella Phage fHe-Kpn01

“…Treatment of the fHe-Kpn01 genomic DNA with S1 nuclease, a nuclease that recognizes single-stranded DNA, indeed indicated the presence of a nick in the genome of fHe-Kpn01, which probably corresponds to nucleotide position 7873 as indicated by PhageTerm ( Figure S3). A nick in the genome is also observed in, among others, siphoviruses T5 [64] and BF23 [65], and podoviruses tf [66], ϕkF77 [67] and LIMElight [68]. Since nicks are present in the genome of several phages, it is important to have a critical look at the output generated by PhageTerm, especially when multiple peaks are present, to prevent an incorrect annotation of the genomic termini.…”

Novel segregation patterns of infecting-mutant genotypes in plate complementation tests among amber mutants of bacteriophage BF23

“…Bacteriophages BF23 and T5 are closely related and possess several unique features by which they can be distinguished from the other coliphages (for reviews, see references 22 and 30). Both phages contain several interrupted phosphodiester bonds at the specific sites of one of the double-stranded, linear DNA molecules (1,12,17,29,31,32). After adsorption, transfer of phage DNA into the host cells takes place by a two-step mechanism (17, 19-21, 24, 32).…”

Physical map of bacteriophage BF23 DNA: restriction enzyme analysis

“…Further digestion led to the loss of fragments 5 and 18. The order of fragments 13, 23, 25, and 27, which are present in two copies because of the terminal repetition in BF23 DNA (5), has been determined by an analysis of T5-BF23 hybrid genomes and will be described in another publication.…”