Fig. 8.

Sequences of insertion sites of the MPME1 and MPME2. (a) The MPME1 insertion in phage BPs and the MPME2 insertion in phage Halo are at different genome locations, and the near-identity of the two genomes in these locations enables elucidation of the pre-integration target sequences. The boxed sequences in BPs and Halo correspond to the DNA sequences that are present in one genome but absent in the other, with the sequences of the junctions shown. Each insertion contains 11 bp inverted repeats (IR-L and IR-R; bold type) of which 10 bp are symmetrically positioned. Phages PMC (and the very close relative Boomer, not shown), Tweety (and its very close relative Llij, not shown), Pacc40, Che8 and Corndog all contain identical copies of the MPME1 present in BPs, although the right of Corndog is deleted. PMC and Tweety are related genomes, and the left-side target sequences are identical, suggesting that these are derived from the same initial integration event; the right-side sequences are different, which further suggests that there have been additional rearrangements. Corndog contains a truncated copy of the element in which the 3′ end of the element is missing 76 bp. Fruitloop contains a copy of MPME2 that is identical to that in Halo and also shares the same 6 bp immediately left of IR-L. The sequence of the element is shown in italics, and the flanking TGA codon in Corndog that terminates the putative TnpA protein is underlined. (b) Brujita and Che9c are related genomes, and Brujita contains an MPME1 element 99 % identical to that in BPs. The flanking sequences in Che9c are near-identical (with the exception of the position immediately to the right of IR-R in the insertion in Brujita), and the boxed sequence represents that which is present in Brujita and absent from Che9c. (c) The pre-integration site corresponding to the insertion in Che8 is not known. However, phage Bxz1 contains a common 110 bp region (shaded box) ∼90 % identical to the left side of the Che8 insertion, and the sequence alignment stops precisely at a position corresponding to 6 bp to the left of the left inverted repeat. At the right end, Che8 and Omega share ∼200 bp of near sequence identity that matches precisely to the end of the right inverted repeat (shaded box). Omega coordinates: 50 716-50 497; Che8 coordinates: 51 089–51 308.