Bacteriophage P2, scientific name Peduovirus P2 (formerly Escherichia virus P2), is a temperate phage that infects E. coli. It is a tailed virus with a contractile sheath and is thus classified in the genus Peduovirus (formerly P2likevirus), family Peduoviridae within class Caudoviricetes. This genus of viruses includes many P2-like phages as well as the satellite phage P4.
Discovery Bacteriophage P2 was first isolated by G. Bertani from the Lisbonne and Carrère strain of E. coli in 1951.Bertani, G., STUDIES ON LYSOGENESIS I.: The Mode of Phage Liberation by Lysogenic Escherichia coli1. Journal of Bacteriology, 1951. 62(3): p. 293. Since that time, a large number of P2-like prophages (e.g. 186, HP1, HK239, and WΦ) have been isolated that shared characters such as host range, serological relatedness and inability to recombine with phage λ, and they seemed to be quite common in E. coli populations as about 30% of the strains in the E. coli reference collection (SABC) contain P2-like prophages .Nilsson, A.S., J.L. Karlsson, and E. Haggård-Ljungquist, Site-specific recombination links the evolution of P2-like coliphages and pathogenic enterobacteria. Molecular Biology and Evolution, 2004. 21(1): p. 1-13. Of these P2-like prophages is P2 best characterized. The P2 phage was found to be able to multiply in many strains of E. coli, as well as in strains of many other species including Serratia, Klebsiella pneumoniae, and Yersinia sp,Haggård-Ljungquist, E., C. Halling, and R. Calendar, DNA sequences of the tail fiber genes of bacteriophage P2: evidence for horizontal transfer of tail fiber genes among unrelated bacteriophages. Journal of Bacteriology, 1992. 174(5): p. 1462-1477. which suggested that it played an important role in horizontal gene transfer in bacterial evolution.
Genome and morphology Phage P2 has a double stranded DNA genome packaged in an icosahedral capsid with a diameter of 60 nanometers that is connected to a 135 nanometer long tail. Presence of phage P4 can cause P2 to form smaller capsids. The tail ends in a baseplate which is the control hub for phage infectivity. The baseplate includes 6 tail fibers which initially bind to receptors on the bacterial cell wall and a tail spike protein that subsequently binds irreversibly to other receptors on the cell wall.
The genome of bacteriophage P2 is 33,592 bp of double-stranded, linear DNA with cohesive ends (accession number AF063097). The 42 genes in the genome can be divided in three main categories: (i) genes required for lytic growth, (ii) genes involved in establishing and maintaining lysogeny (such as int and C), and (iii) the nonessential genes (including old, tin, and Z/fun). Furthermore, a number of open reading frames (ORFs) is found in P2 genome, which may encode functional proteins.
Life cycle Bacteriophage P2 is a temperate phage, which means that it can propagate lytically (i.e. directing the host cell to produce phage progenies and finally lysing the host when the phage progenies exit), as well as establish lysogeny (i.e. injecting and fusing its genetic material into the genome of the host without lysing the cell) and maintain as a prophage in host genome.
Infection Adsorption of the virion to the host cell is the key step in phage infection, which is essential for the following phage binding and injection of phage DNA . During the adsorption process, the tail fiber of phage P2 recognizes and binds to the core region of the lipopolysaccharide of E. coli, and then the phage would inject its DNA into the cytoplasm.Haggård-Ljungquist, E., C. Halling, and R. Calendar, DNA sequences of the tail fiber genes of bacteriophage P2: evidence for horizontal transfer of tail fiber genes among unrelated bacteriophages. Journal of Bacteriology, 1992. 174(5): p. 1462-1477.
Lytic cycle Early transcription The gene expression of P2 is regulated over time during the lytic cycle. Early transcription, which is responsible for the expression of the genes required for the following DNA replication, is initiated immediately after infection. The early operon contains 9 genes and transcribes from the lytic promotor Pe. The first gene in the operon, designated cox, encodes the repressor of the lysogenic promoter Pc and prevent the expression of the genes required for establishing lysogeny.Saha, S., E. Haggård-Ljungquist, and K. Nordström, The cox protein of bacteriophage P2 inhibits the formation of the repressor protein and autoregulates the early operon. The EMBO Journal, 1987. 6(10): p. 3191.Nilsson, A., and E. Haggård-Ljungquist. The P2-like bacteriophages. In R. Calendar (ed.), The bacteriophages. Oxford Press, Oxford, 2005: p. 365-390 Then the phage enters the lytic lifecycle and early transcription starts. Only host σ70 RNA polymerase is required in the early transcription process.
DNA replication Besides cox, the early operon contains two other genes which are essential for P2 DNA replication, genes A and B.Lindahl, G., Genetic map of bacteriophage P2. Virology, 1969. 39(4): p. 839-860Lindqvist, B.H., Vegetative DNA of temperate coliphage P2. Molecular and General Genetics, 1971. 110(2): p. 178-196. Replication of P2 genome is initiated by A protein and takes place from a fixed origin (ori) via a modified rolling-circle mechanism that generates double-stranded monomeric circles.Liu, Y. and E. Haggård-Ljungquist, Studies of bacteriophage P2 DNA replication: localization of the cleavage site of the A protein. Nucleic Acids Research, 1994. 22(24): p. 5204-5210.Odegrip, R. and E. Haggård-Ljungquist, The two active-site tyrosine residues of the A protein play non-equivalent roles during initiation of rolling circle replication of bacteriophage P2. Journal of Molecular Biology, 2001. 308(2): p. 147-163. The B protein may be required for lagging-strand synthesis, as it can interact with E. coli DnaB and function as a helicase loader.Odegrip, R., et al., The interaction of bacteriophage P2 B protein with Escherichia coli DnaB helicase. Journal of Virology, 2000. 74(9): p. 4057-4063.
Activation of late transcription Late gene transcription is initiated from four late promoters once DNA replication has started and the transcriptional activator Ogr has been expressed.Wood, L.F., N.Y. Tszine, and G.E. Christie, Activation of P2 late transcription by P2 ogr protein requires a discrete contact site on the C terminus of the α subunit of Escherichia coli RNA polymerase. Journal of Molecular Biology, 1997. 274(1): p. 1-7.Mandali, S., Site-specific recombination of P2-like phages; possible tools for safe gene therapy: A focus on phage ΦD145. 2010. The late promoters, PP, PO, PV and PF, are activated by Ogr and direct the transcription of the genes responsible for lytic functions as well as encoding building blocks for phage progenies.Birkeland, N.K. and B.H. Lindqvist, Coliphage P2 late control gene ogr: DNA sequence and product identification. Journal of Molecular Biology, 1986. 188(3): p. 487-490.Christie, G.E., et al., Regulation of bacteriophage P2 late-gene expression: the ogr gene. Proceedings of the National Academy of Sciences, 1986. 83(10): p. 3238-3242. All the four promoters have a region with a partial dyad symmetry centered around 55 bp downstream from the transcriptional initiation site. Revealed by deletion analysis and base substitutions, this dyad symmetry has been shown to be essential for promoter activity.Grambow, N.J., et al., Deletion analysis of a bacteriophage P2 late promoter. Gene, 1990. 95(1): p. 9-15.Van Bokkelen, G., et al., Mutational analysis of a bacteriophage P4 late promoter. Journal of Bacteriology, 1991. 173(1): p. 37-45. Moreover, the late genes of P2 can also be activated by the δ proteins of satellite phages P4 and ΦR73 directly.Clerch, B., E. Rivera, and M. Llagostera, Bacteriophage PSP3 and phi R73 activator proteins: analysis of promoter specificities. Journal of Bacteriology, 1996. 178(19): p. 5568-5572.
Lysis During the lytic cycle, similar to other double-stranded phages, bacteriophage P2 applies a holin-endolysin system to lyse the host cell. P2 have two essential lysis genes (gene K and gene Y) and two ancillary lysis genes (lysA and lysB).Ziermann, R., et al., Functions involved in bacteriophage P2-induced host cell lysis and identification of a new tail gene. Journal of Bacteriology, 1994. 176(16): p. 4974-4984. The product of K gene has extensive amino acid sequence similarity to that of gene R in λ phage, which exhibits endolysin function and attack the glycosidic bond. Gene Y encodes a polypeptide sharing high similarity to the holin protein family, which forms ‘holes’ in the cell membrane and provide a pathway for endolysin escape to the cell wall. The nonessential genes, lysA and lysB, seem to play a role in controlling the correct timing of lysis.Zimecki, M., et al., Bacteriophages provide regulatory signals in mitogen-induced murine splenocyte proliferation. Cell Mol Biol Lett, 2003. 8(3): p. 699-711.
Lysogenic cycle
Prophage integration During lysogenic cycle, P2 genome is inserted into the host chromosome and maintained as a prophage. The integration involves site-specific recombination between a bacterial attachment site (attB) and a phage attachment site (attP), which generates host-phage junctions, attL and attR. This reaction is controlled by a phage-encoded integrase, and leads to no gain or loss of nucleotides. Another integration host factor, IHF, is also essential in the integration process and serves as an architectural protein that binds and bends DNA.Yu, A. and E. Haggård-Ljungquist, Characterization of the binding sites of two proteins involved in the bacteriophage P2 site-specific recombination system. Journal of Bacteriology, 1993. 175(5): p. 1239-1249. Thus, the integration mechanism of phage P2 is similar to the well-studied λ site-specific recombination system, but the phage proteins and their DNA binding sites differ.Landy, A., Dynamic, structural, and regulatory aspects of lambda site-specific recombination. Annual Review of Biochemistry, 1989. 58(1): p. 913-941.
Maintenance of lysogeny The lysogenic state of P2 is promoted and maintained by the C repressor. It is a 99-amino acids polypeptide and binds to only one operator region which regulates the expression of the early genes: cox, B and possibly A. Research has shown that C repressor can both positively and negatively regulate its own Pc promoter as Pc is up regulated at low C level and down regulated at high levels.Saha, S., B. Lundqvist, and E. Haggård-Ljungquist, Autoregulation of bacteriophage P2 repressor. The EMBO Journal, 1987. 6(3): p. 809. Since the C repressor is not inactivated by the SOS/RecA system of E. coli, the P2 prophage is non-inducible by ultraviolet irradiation. Furthermore, even if C repressor is inactivated, the P2 prophage is unable to excise, due to lack of int expression.Bertani, L.E., Abortive induction of bacteriophage P2. Virology, 1968. 36(1): p. 87-103. Hence, P2 has been regarded as the prototype for the non-inducible class of temperate phages. The mechanism about how P2 solve the induction-excision paradox still remains unknown.
Control of lytic versus lysogenic growth