An integrase clade that repeatedly targets prophage late genes, yielding helper-embedded satellites

Satellites are mobile genetic elements that rely on helper phages for their mobilization. The many known satellite-helper interactions are trans-regulatory, with gene products from one partner modulating the nucleic acid or protein activities of the other. We discovered a satellite type with a more intimate cis-regulatory configuration: integrated within, and co-oriented with, a late gene of its lambdoid helper prophage. This helper-embedded satellite (HES) configuration would delay expression of the interrupted helper late gene until the satellite excises; it also offers potential passive components to both HES replication and late transcription, driven by the helper. Induction of a helper-satellite composite was monitored; precise excision of the entire composite was observed, followed by its replication, and the excision of the satellite from it. We mapped 491 HESs to one of 14 sites in cognates of phage lambda late genes A, B, C, E, V, T, H, L and J. The associated integrases form a single phylogenetic clade with subclades respecting the 14 site groups, while the attP attachment site regions contained a new doubled DNA sequence motif. This clade thus exhibits a repeated tropism for prophage late genes as it develops new integration sites. HESs bear close genomic similarities to gram-negative phage-induced chromosomal islands (PICIs, of which we found many more integrated into fis and hpt genes). We describe four ordered zones in a general HES/PICI genome organization: an integration zone encoding integrase and AlpA, a Bro zone encoding members of the Bro-N network of domain-swapping DNA-interactive proteins and immunity repressor RNAs, a replication zone, and a late zone in which clusters as large as 18 consecutive helper late genes have been captured. Like the late zone, the Bro zone is dynamic, perhaps due to activity of the Bro proteins themselves.