Extended Data Fig. 2: ΦAP1.1 lysogenization location.
We decided to look for integration of ΦAP1.1 in other genomic sites with the 8-bp sequence of the attB present on the CRISPR repeat. Because strain K56 is not sequenced and therefore we could not identify such sequences, we decided to perform experiments with strain SF370, which harbors an additional 27 sites with the attB sequence. To do this, we infected strain CEM1ΔΦ[Δ2-5], which lacks the prophages as well as most spacers of the CRISPR array (in particular spc4, which targets ΦAP1.1) present in SF370. We isolated and analyzed 110 spectinomycin-resistant colonies and looked for the presence of the phage (p) and its integration attL site (i) via PCR. We found that all prophages were inserted into the CRISPR array (in different repeats, generating different sizes for the attL PCR products). This result indicates a strong preference for integration into the repeat sequences and also suggests that regions outside of the 8-bp attB site are important for integration. Agarose gel electrophoresis of the attL (i) or phage (p) PCR products obtained after selection of individual spectinomycin-resistant ΦAP1.1 lysogens. PCRs for individual lysogens are divided by black lines.
