The Φ24B ::Kan genome is 57.6 kb in size and is identical in all aspects to its wild-type parental phage other than the stxA gene interruption [14, 18]. The majority of genes and coding sequences (CDS) carried by Φ24B are simply annotated as hypothetical [GenBank: HM_208303]. Bacteriophages tightly regulate expression of their genes involved in maintenance
of lysogeny versus replication of viral progeny, and the differentiation of gene expression associated with each state needed to be carefully Temsirolimus chemical structure determined in order to definitively associate expressed proteins and their genes with either the temperate or the lytic cycle. Results The rate of spontaneous lysis in an E. coli MC1061(Φ24B) culture at different stages of growth Spontaneous induction, defined as the induction of prophages from lysogens in the absence of an applied stimulus , occurs constantly in a proportion of the lysogen population in any culture, and this could seriously interfere with the differentiation of gene expression between lytic and lysogenic states. In this study, it was necessary to determine culture conditions under which the number of spontaneous PFT�� induction events was low whilst the cell density was high, enabling the consistent harvesting of sufficient
amounts of cell-associated protein for downstream analyses. Lysogen cultures were sampled at hourly intervals beginning two hours post inoculation, and the c.f.u. ml-1 and p.f.u. ml-1 determined. The lowest ratio of infective phages to cells, 1:50, occurred at both 2 h and 3 h of lysogen growth. However the c.f.u. ml-1 during these times was relatively low; OD600 = 0.184 (± 0.003) and OD600 = 0.651 (± 0.008), respectively. The ratio Sorafenib nmr of phage to host cells increased sharply after 4 h of growth, before dropping after 5 h to 1:33 (OD600 = 1.192 [± 0.011]). The ratio of phage to cells in the culture remained stable at 1:33 through to 6 hours of growth. Lysogen growth conditions
were therefore standardised for MC1061 (Φ24B) at 5-6 hours when the cells were grown to an OD600 of 1.2-1.3. Phage-encoded, lysogen-culture gene expression identified by CMAT A total of 13,519 clones were subjected to CMAT primary screening, and taking efficiency of the library into account, this equates to a 3.3x coverage of the phage genome. Of these, 330 were identified by the lysogen-specific antiserum and chosen for further analyses and secondary screening. After two rounds of secondary screening, 250 clones were removed from the study and PCR analysis of the remaining 80 clones demonstrated that 46 possessed vector DNA only. The remaining 34 recombinant transformants produced a peptide recognised by antibodies in the lysogen specific antiserum. The cloned inserts were sequenced, and the DNA sequences translated in all six possible reading frames. Twenty-three of the clones possessed sequences from twenty different Φ24B CDS (Table 1, Figure 1).