Bacteriophage Ø29 protein p6: an architectural protein involved in genome organization, replication and control of transcription

Abstract

Protein p6 of B. subtilis bacteriophage Ø29 binds to DNA forming a nucleoprotein complex in which the DNA wraps a protein core forming a right-handed superhelix, therefore restraining positive supercoiling and compacting the DNA. The protein does not specifically recognize a nucleotide sequence but rather a structural feature and it binds as a dimer through the minor groove. Protein p6 is in a monomer-dimer equilibrium that shifts to higher-order structures at a concentration of about 1 mM. These structures are probably present in vivo as the intracellular concentration of p6 is estimated to be in this range, and in fact the effective concentration should be still higher due to the macromolecular crowding. The p6 oligomers show an elongated shape compatible with a helical structure reminiscent of the superhelical DNA of the nucleoprotein complex, therefore it was proposed that protein p6 forms a scaffold on which the DNA folds. Since protein p6 is very abundant in infected cells, enough to bind the entire viral progeny, it was proposed to have an architectural role organizing and compacting the viral genome. It has been demonstrated that protein p6 binds in vivo to most, if not all, the Ø29 genome, although with different affinity, the highest one corresponding to the genome ends. Binding to plasmidic DNA was much lower, although it increased dramatically when the negative superhelicity was decreased. Hence, protein p6 binding specificity for Ø29 DNA is based on supercoiling, providing that the Ø29 genome, although topologically constrained, has a negative superhelicity lower than that of plasmid DNA. The formation of the nucleoprotein complex has functional implications in DNA replication and the control of transcription. It activates the initiation of replication that occurs at the genome ends for which the binding affinity is highest. It represses early transcription from promoter C2, and, together with protein p4, it represses transcription from promoters A2b and A2c and activates late transcription from promoter A3; therefore, protein p6 is involved in the early to late transcription switch.

DNA bending and looping in the transcriptional control of bacteriophage φ29

“…The synthesis of p6 results in the activation of the initiation of viral DNA synthesis and in the repression of early promoters A2b, A2c and C2. Protein p6 binds in a nonsequence specific manner, but preferentially to bendable sequences of the phage DNA, forming extended multimeric complexes (Serrano et al, 1989;González-Huici et al, 2004). The multimeric complex formed at the right end of the genome represses promoter C2 Camacho & Salas, 2001a).…”

Requirements for Bacillus subtilis bacteriophage Φ29 DNA ejection

“…The viral genome is compacted and organized by protein p6, an abundant viral protein that binds DNA with little sequence-specificity and strong supercoiling dependency (González-Huici et al, 2004b) forming a nucleoprotein complex in which a multimeric protein core is wrapped by a DNA right-handed superhelix (Serrano et al, 1993). This conformational change has functional implications, thus, it is absolutely required for viral DNA replication and is involved in transcriptional control as it represses early promoters C2, A2b and A2c and activates late promoter A3 (reviewed in González-Huici et al, 2004c). We took advantage of the binding properties of viral protein p6 to monitor the entry of Φ29 DNA into the cell.…”

Molecular Interactions and Protein-Induced DNA Hairpin in the Transcriptional Control of Bacteriophage Ø29 DNA

“…Protein p4 binds to specific target sites and is required for the activation of the late promoter A3 and for the repression of early promoters A2b and A2c [44]. Protein p6 is a nucleoid-type protein that binds in a non-sequence specific manner to the phage DNA, generating large nucleoprotein complexes [50,51]. The p6-DNA complex formed at the right end of the genome represses promoter C2 [52,53].…”