Previous studies have shown that infection of Prochlorococcus MED4 by the cyanophage P-SSP7 leads to increased transcript levels of host endoribonuclease (RNase) E. However, it has remained enigmatic whether this is part of a host defense mechanism to degrade phage messenger RNA (mRNA) or whether this single-strand RNA-specific RNase is utilized by the phage. Here we describe a hitherto unknown means through which this cyanophage increases expression of RNase E during phage infection and concomitantly protects its own RNA from degradation. We identified two functionally different RNase E mRNA variants, one of which is significantly induced during phage infection. This transcript lacks the 59 UTR, is considerably more stable than the other transcript, and is likely responsible for increased RNase E protein levels during infection. Furthermore, selective enrichment and in vivo analysis of double-stranded RNA (dsRNA) during infection revealed that phage antisense RNAs (asRNAs) sequester complementary mRNAs to form dsRNAs, such that the phage protein-coding transcriptome is nearly completely covered by asRNAs. In contrast, the host protein-coding transcriptome is only partially covered by asRNAs. These data suggest that P-SSP7 orchestrates degradation of host RNA by increasing RNase E expression while masking its own transcriptome from RNase E degradation in dsRNA complexes. We propose that this combination of strategies contributes significantly to phage progeny production.KEYWORDS antisense RNA; T7-like cyanophage P-SSP7; dsRNA fishing; RNase E; Prochlorococcus A common theme of the lifestyle of viruses is the manipulation of host metabolism for the purpose of viral reproduction. However, different virus types have established different regulatory pathways for the takeover and manipulation of their particular hosts. For example, all genes of T4 and the early genes of T7 Escherichia coli bacteriophages are transcribed by the host RNA polymerase (RNAP) (Ueno and Yonesaki 2004;Molineux 2006). However, expression of middle and late T4 genes is mediated by host RNAP that has been modified by T4-encoded factors (Ueno and Yonesaki 2004). In contrast to T4, the subsequent T7 expression program is coordinated by the activity of a phage RNAP (Maniloff and Ackermann 1998). Nevertheless, direct manipulation of host proteins plays a crucial role for the gene expression program of T7.The gene product of the early T7 0.7 gene codes for a protein kinase (Rahmsdorf et al. 1974) and is responsible for phosphorylation and, thus, functional manipulation of .90 host proteins (Robertson et al. 1994). For example, phosphorylation of host RNAP b9-subunit (Zillig et al. 1975) results in reduced processivity, which is believed to assist in the coordinated transition of expression from T7 cluster 1 to cluster 2 genes (Severinova and Severinov 2006). In addition, phosphorylation of translation factors such as IF1, IF2, and IF3 is required for expression of T7 cluster 3 genes (Robertson and Nicholson 1992).Another protein of particul...