Multiple novel promoters from the early region in the Streptomyces temperate phage φC31 are activated during lytic development

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Abstract
Summary: Evidence is presented that transcription of most of the early genes in the Streptomyces coelicolor A3(2) phage φC31 is from a series of unusual promoters that depend on a function expressed early in the φC31 lytic cycle. Primer extension analysis on the 5′ ends of three early mRNAs, from samples prepared 10min after induction of a thermosensitive φC31 lysogen, showed that the 5′ ends all mapped close to highly similar sequences, which are proposed to be an important part of phage‐specific promoters. In a shotgun cloning experiment, a fragment containing one of these sequences strongly activated transcription of the xylE reporter gene in plaques of a φC31‐derived promoter‐probe vector. Another of the sequences was inserted into a xylE‐containing promoter‐probe plasmsid vector, and promoted xylE expression only when the host was supporting the lytic cycle of φ C31. This suggested that a transcription factor needed for activity of the promoters was present only in φC31 ‐infected cells. Examination of published and unpublished φ C31 sequence data revealed several more sequences that closely resemble the conserved region of the characterized promoters. Most of these are found in positions close to apparent transcription start sites mapped previously by low‐resolution S1 mapping. An overall consensus sequence for the conserved region suggests a general organization (though not a primary sequence) resembling that of promoters recognized in other bacteria by the σ;54 form of RNA polymerase.