Phage P1

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Bacteriophage P1 Phage P1 was isolated in 1951 by Giuseppe Bertani from the Escherichia coli strain of Lisbonne and Carrere. [1]. P1 has been widely used to construct new batcterial strains and was used extensively to map the Escherichia Coli chromosome. P1 has served as a model organism for different aspects of phage and biology such as DNA restriction modification[2][3],site-specific recombination[4], plasmid replication[5], partition[6], incompatibility[7] and addiction[8]

Morphology

Phage P1 exhibits the classical bacteriophage morphology with an icosahedral head, 220nm long inflexible tail with a complete tube surrounded by a contractile sheath, baseplate and six kinked tail fibers. The icosahedral head contains the phage genome. A variable part(encoded by an invertible segment of P1 DNA) of the tail fibers(1 to 2nm thick) determines the specificity of P1 adsorption on different hosts.[9]

Genome Organization

AF234172.1 on NCBI AF234173.1 on NCBI

<gbrowseImage> name=NC_005856:44,801..94,800 source=bacteriophage_P1 width=800 type=Genes </gbrowseImage>

The genome of P1 is about 94 kb with atleast 117 genes that are organized in 45 operons. Protein-coding genes occupy 92% of the genome. 4 of the 45 operons are responsible for the choice between lysis and lysogeny and another 4 are responsible for plasmid maintenance. The remaining 37 are invovled in lytic development. Regulatory regions of 38 operons contain one or more sequences that resemble strong δ70 promoters. In the virion, DNA is double stranded, linear, terminally redundant and circularly permuted. The terminal redundant region is important because foreign pieces of DNA can be inserted in non-essential regions.

Life cycle

Lytic cycle

Adsorbtion and Injection

The terminal glucose of the lipopolysaccharide core of the bacterial outer membrane acts as a P1 receptor.[10] The tail fibers of the P1 phage promote the recognition of the host bacterium. At least three of the six tail fibers with specific receptor molecules are sufficient enough to trigger the injection mechanism[11]. The precise mechanism of mechanism of penetration is not known but models[12] suggest that the phage tail contracts, the tail tube is pushed through the baseplate puncturing the outer cell membrane along with the bacterial cell wall. A lytic transglycosylase faclitates the puncture of the bacterial cell wall[13]. The content of the phage head is then injected into the periplasm of the host cell that is mediated by an uncharacterized pore. Another mechanism that is of interest is the sim superinfection exclusion system. Sim is rapidly expressed immediately after infection in the innermembrane or the periplasmic space of the infected host cell[14]. The proposed hypothesis is that the Sim protein traps superinfecting P1 genomes in the periplasm, so that it does not interfere with ongoing P1 infection cycle[15]. Since the P1 genome is linear, it needs to rapidly circularized upon entering the host cytoplasm before it is degradaded by cellular nucleases[16]. The mechanism of this is still unknown but it is proposed that it is mediated by Cre-dependent site-specific recombination using the presence of two lox-Cre sites in some phage genomes[17]. A list of uncharacterized mechanisms that could be invovled. A recent paper[18] that engineered tiny E.coli host cells has shown three configurations: extended tail stage with DNA present in the phage head, a contracted tail stage with DNA and a contracted tail stage without DNA. They have also shown that there is a uniform penetration of the inner tail tube into the E.coli periplasm and a significant movment of the baseplate from the outer membrane during tail contraction.

Early gene expression

Middle gene expression

DNA replication

The minimal P1 replicon has an open reading frame for the essential replication protein RepA, flanked by two sets of multiple 19-base pair repeated sequences, incA and incC along with the origin of plasmid replication. Binding of RepA to the iterons in incC is required for initiation while binding of repA to incA iterons serves to control the plasmid copy number. Host factors contribute to the initiation of oriR and four GATC dam methylation sites within the origin itself need to be methylated[19] [20] [21]. DNA melting occurs through concerted action of RepA and host factors : DnaA and HU [22], [23]. The repA promoter is located within incC and is expressedn when repA binds to the interons [24]. RepA protein exists as dimers when freshly synthesized but it needs to be a monomer to have DNA-binding activity. DnaK, DnaJ and GrepE chaperones are required to convert the dimers into active monomers[25] [26] [27] [28]

Late gene expression

Packaging

The packing of bacteriophage into viral capsids occurs by a well-ordered process that preferentially selects viral chromosomes for encapsidation from a pool of DNA that consists of mostly host DNA sequences. A common feature of DNA packing is empty protein shells that interact with viral DNA that is mediated by phage-encoded DNA recognition and processing proteins. 'pac' is the site on the viral DNA which the proteins bind.

Lysis

Lysogenic state

Lysis-Lysogeny switch

Prophage induction

See also

References

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  1. ↑ BERTANI, G (1951) Studies on lysogenesis. I. The mode of phage liberation by lysogenic Escherichia coli. J. Bacteriol. 62 293-300 PubMed
  2. ↑ ARBER, W & DUSSOIX, D (1962) Host specificity of DNA produced by Escherichia coli. I. Host controlled modification of bacteriophage lambda. J. Mol. Biol. 5 18-36 PubMed
  3. ↑ DUSSOIX, D & ARBER, W (1962) Host specificity of DNA produced by Escherichia coli. II. Control over acceptance of DNA from infecting phage lambda. J. Mol. Biol. 5 37-49 PubMed
  4. ↑ Hamilton, DL & Abremski, K (1984) Site-specific recombination by the bacteriophage P1 lox-Cre system. Cre-mediated synapsis of two lox sites. J. Mol. Biol. 178 481-6 PubMed
  5. ↑ Chattoraj, DK (2000) Control of plasmid DNA replication by iterons: no longer paradoxical. Mol. Microbiol. 37 467-76 PubMed
  6. ↑ Austin, S & Abeles, A (1983) Partition of unit-copy miniplasmids to daughter cells. I. P1 and F miniplasmids contain discrete, interchangeable sequences sufficient to promote equipartition. J. Mol. Biol. 169 353-72 PubMed
  7. ↑ Sternberg, N et al. (1981) Group Y incompatibility and copy control of P1 prophage. Plasmid 5 138-49 PubMed
  8. ↑ Lehnherr, H et al. (1993) Plasmid addiction genes of bacteriophage P1: doc, which causes cell death on curing of prophage, and phd, which prevents host death when prophage is retained. J. Mol. Biol. 233 414-28 PubMed
  9. ↑ Łobocka, MB et al. (2004) Genome of bacteriophage P1. J. Bacteriol. 186 7032-68 PubMed
  10. ↑ Sandulache, R et al. (1984) Cell wall receptor for bacteriophage Mu G(+). J. Bacteriol. 160 299-303 PubMed
  11. ↑ Crawford, JT & Goldberg, EB (1980) The function of tail fibers in triggering baseplate expansion of bacteriophage T4. J. Mol. Biol. 139 679-90 PubMed
  12. ↑ Dreiseikelmann, B (1994) Translocation of DNA across bacterial membranes. Microbiol. Rev. 58 293-316 PubMed
  13. ↑ Lehnherr, H et al. (1998) Penetration of the bacterial cell wall: a family of lytic transglycosylases in bacteriophages and conjugative plasmids. Mol. Microbiol. 30 454-7 PubMed
  14. ↑ Maillou, J & Dreiseikelmann, B (1990) The sim gene of Escherichia coli phage P1: nucleotide sequence and purification of the processed protein. Virology 175 500-7 PubMed
  15. ↑ Kliem, M & Dreiseikelmann, B (1989) The superimmunity gene sim of bacteriophage P1 causes superinfection exclusion. Virology 171 350-5 PubMed
  16. ↑ Sternberg, N et al. (1986) Bacteriophage P1 cre gene and its regulatory region. Evidence for multiple promoters and for regulation by DNA methylation. J. Mol. Biol. 187 197-212 PubMed
  17. ↑ Hochman, L et al. (1983) Site-specific recombinational circularization of bacteriophage P1 DNA. Virology 131 11-7 PubMed
  18. ↑ Liu, J et al. (2011) Visualization of bacteriophage P1 infection by cryo-electron tomography of tiny Escherichia coli. Virology 417 304-11 PubMed
  19. ↑ Abeles, A et al. (1993) Evidence of two levels of control of P1 oriR and host oriC replication origins by DNA adenine methylation. J. Bacteriol. 175 7801-7 PubMed
  20. ↑ Abeles, AL & Austin, SJ (1988) P1 plasmid replication requires Escherichia coli Dam-methylated DNA. Gene 74 185-6 PubMed
  21. ↑ Brendler, T et al. (1991) Critical sequences in the core of the P1 plasmid replication origin. J. Bacteriol. 173 3935-42 PubMed
  22. ↑ Mukhopadhyay, G et al. (1993) Open-complex formation by the host initiator, DnaA, at the origin of P1 plasmid replication. EMBO J. 12 4547-54 PubMed
  23. ↑ Wickner, S et al. (1990) Deletion analysis of the mini-P1 plasmid origin of replication and the role of Escherichia coli DnaA protein. J. Biol. Chem. 265 11622-7 PubMed
  24. ↑ Mukhopadhyay, S & Chattoraj, DK (2000) Replication-induced transcription of an autorepressed gene: the replication initiator gene of plasmid P1. Proc. Natl. Acad. Sci. U.S.A. 97 7142-7 PubMed
  25. ↑ DasGupta, S et al. (1993) Activation of DNA binding by the monomeric form of the P1 replication initiator RepA by heat shock proteins DnaJ and DnaK. J. Mol. Biol. 232 23-34 PubMed
  26. ↑ Skowyra, D & Wickner, S (1993) The interplay of the GrpE heat shock protein and Mg2+ in RepA monomerization by DnaJ and DnaK. J. Biol. Chem. 268 25296-301 PubMed
  27. ↑ Sozhamannan, S & Chattoraj, DK (1993) Heat shock proteins DnaJ, DnaK, and GrpE stimulate P1 plasmid replication by promoting initiator binding to the origin. J. Bacteriol. 175 3546-55 PubMed
  28. ↑ Wickner, S et al. (1992) DnaJ, DnaK, and GrpE heat shock proteins are required in oriP1 DNA replication solely at the RepA monomerization step. Proc. Natl. Acad. Sci. U.S.A. 89 10345-9 PubMed
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