The Role of RNA Polymerase σ Subunit in Promoter-Independent Initiation of Transcription

In bacteria, initiation of transcription depends on the RNA polymerase σ subunit, which brings catalytically proficient RNA polymerase core to promoters by binding to specific DNA elements located upstream of the transcription start point. Here, we study σ-dependent synthesis of a transcript that is used to prime replication of the single-stranded genome of bacteriophage M13. We show that, in this system, σ plays no role in DNA recognition, which is accomplished solely through RNA polymerase core interaction with DNA downstream of the transcription start point. However, σ is required for full-sized transcript synthesis by allowing RNA polymerase core to escape into productive elongation. RNA polymerase σ may play a similar role during replication primer synthesis in other bacterial mobile elements whose life cycle involves a single-stranded DNA stage.