The phi29 transcriptional regulator contacts the nucleoid protein p6 to organize a repression complex.

The nucleoid protein p6 of Bacillus subtilis phage phi29 binds to DNA, recognizing a structural feature rather than a specific sequence. Upon binding to the viral DNA ends, p6 generates an extended nucleoprotein complex that activates the initiation of phi29 DNA replication. Protein p6 also participates in transcription regulation, repressing the early C2 promoter and assisting the viral regulatory protein p4 in controlling the switch from early to late transcription. Proteins p6 and p4 bind cooperatively to an approximately 200 bp DNA region located between the late A3 and the early A2c promoters, generating an extended nucleoprotein complex that helps to repress the early A2c promoter and to activate the late A3 promoter. We show that stable assembly of this complex requires interaction between protein p6 and the C-terminus of protein p4. Therefore, at this DNA region, stable polymerization of protein p6 relies on p4-specified signals in addition to the structural features of the DNA. Protein p4 would define the phase and boundaries of the p6-DNA complex.