Phage PRD1

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Bacteriophage PRD1 is a member of the Tectiviridae family[1] and is closely related to the other lipid-containing phages PR3, PR4, PR5, and L17[2]. It is a plasmid-dependent phage that has been shown to infect a variety of gram-negative hosts, including Escherichia coli, with the requirement that hosts contain incompatibility group plasmids P, W, or N[3]. Notably, PRD1 has 110 bp inverted terminal repeats[4] and a covalently bound terminal protein on the 5' ends[5] of the 14,927bp genome.

The full sequence is available from NCBI as NCBI Reference Sequence: NC_001421.2


Morphology

Phage PRD1, like the other Tectiviridae, has an inflexible icosahedral protein structure surrounding a lipid membrane[1]. The linear dsDNA is contained inside this lipid-protein vesicle[6]. The phage has a molecular mass of about 66x106 Da; by weight it is 15% DNA, 15% lipid, and the remaining weight is due to protein content[7]. About half of the flexible inner membrane is made of host lipids[1]; the rest of the vesicle consists of viral proteins[8][6]. Cryo-electron microscopic reconstructions of PRD1 show the phage capsid is about 65.5 nm, measured as the diameter between two parallel edges, with a maximum diameter of 69.8nm when measured between vertices[1].

The rigid coat is comprised mainly of the 43.1 kDa[9] protein P3, which forms 240 trimeric units with 6-fold symmetry[10] arranged in β-sheets[11]. A single face of the icosahedron contains 12 copies of the trimeric P3 in a pseudo T=25 lattice[1]. The capsid also contains the 34.3 kDa [9]P5 as the minor coat protein[10], and pentamers of the 13.7kDa P31 form the vertices[12]. The major and minor proteins contribute to the formation of a spike structure at the 12 vertices[12][13]. With P31, the minor coat protein P5 forms an adaptor complex and anchors P2 to form the spike[13]. Protein P2 is required for adsorption to the host, and likely only exists as a single monomer at the distal end of the spike[14][13].

One study has shown the viral capsid can possess a membranous tail 140 Å in diameter that does not seem to be necessary for infection[12].

Genome Organization

159192286 on NCBI

<gbrowseImage> name=NC_001421:1..14927 source=bacteriophage_PRD1 width=800 type=Genes </gbrowseImage>


PRD1 has a linear, 14927 bp genome of dsDNA. The small size of many of the membrane- associated proteins has made characterizing individual proteins difficult[6], and there is no clear consensus as to which of the ORFs encode functional products. There are 31 genes and 31 confirmed or putative proteins as noted by RefSeq [15], but there are about 31 ORFs in the upper strand and 18-19 ORFs in the lower strand[6].

Life cycle

Adsorption and Injection

DNA replication

A unique trait of PRD1 is the protein-primed mechanism of replication.

The replication process starts with a tyrosine residue in the terminal protein forming a phosphodiester bond to the first nucleotide in the nascent DNA chain. The host DNA polymerase uses the protein-DNA complex as a template, and continues to elongate the chain on the 3' end. [16]


http://www.ncbi.nlm.nih.gov/pmc/articles/PMC237855/pdf/jvirol00029-0252.pdf

PMID:8331725[17]

Gene Expression

The earliest proteins are synthesized soon after infection. The "very early" group includes P1, P8, and P12, while the "medium early" group of P12 and P19 is produced slightly later[18]. Fifteen minutes after infection, the late class of proteins is synthesized; this group includes all of the proteins in the virion such as P20, P21, and P22[18].



Packaging

Lysis

Lysis occurs about 60 minutes postinfection[18].

See also


References

See Help:References for how to manage references in EcoliWiki.

  1. ↑ 1.0 1.1 1.2 1.3 1.4 Edited by Richard Calendar (2006) The Bacteriophages (Oxford University Press, Oxford, NY) ISBN 0-19-514850-9
  2. ↑ Bamford, DH et al. (1981) Comparison of the lipid-containing bacteriophages PRD1, PR3, PR4, PR5 and L17. J. Gen. Virol. 57 365-73 PubMed
  3. ↑ Olsen, RH et al. (1974) Characteristics of PRD1, a plasmid-dependent broad host range DNA bacteriophage. J. Virol. 14 689-99 PubMed
  4. ↑ Pakula, TM et al. (1990) Characterization of a DNA binding protein of bacteriophage PRD1 involved in DNA replication. Nucleic Acids Res. 18 6553-7 PubMed
  5. ↑ Bamford, D et al. (1983) Identification of a protein bound to the termini of bacteriophage PRD1 DNA. J. Virol. 47 311-6 PubMed
  6. ↑ 6.0 6.1 6.2 6.3 Bamford, JK et al. (1991) Genome organization of membrane-containing bacteriophage PRD1. Virology 183 658-76 PubMed
  7. ↑ Bamford, DH et al. (1995) Bacteriophage PRD1: a broad host range DSDNA tectivirus with an internal membrane. Adv. Virus Res. 45 281-319 PubMed
  8. ↑ Rydman, PS & Bamford, DH (2002) The lytic enzyme of bacteriophage PRD1 is associated with the viral membrane. J. Bacteriol. 184 104-10 PubMed
  9. ↑ 9.0 9.1 Bamford, JK & Bamford, DH (1990) Capsomer proteins of bacteriophage PRD1, a bacterial virus with a membrane. Virology 177 445-51 PubMed
  10. ↑ 10.0 10.1 Butcher, SJ et al. (1995) DNA packaging orders the membrane of bacteriophage PRD1. EMBO J. 14 6078-86 PubMed
  11. ↑ Bamford, DH et al. (1990) Structural study of the lipid-containing bacteriophage PRD1 and its capsid and DNA components by laser Raman spectroscopy. Biochemistry 29 5982-7 PubMed
  12. ↑ 12.0 12.1 12.2 Rydman, PS et al. (1999) Bacteriophage PRD1 contains a labile receptor-binding structure at each vertex. J. Mol. Biol. 291 575-87 PubMed
  13. ↑ 13.0 13.1 13.2 Caldentey, J et al. (2000) Assembly of bacteriophage PRD1 spike complex: role of the multidomain protein P5. Biochemistry 39 10566-73 PubMed
  14. ↑ Grahn, AM et al. (1999) Stable packaging of phage PRD1 DNA requires adsorption protein P2, which binds to the IncP plasmid-encoded conjugative transfer complex. J. Bacteriol. 181 6689-96 PubMed
  15. ↑ http://www.ncbi.nlm.nih.gov/genome/proteins/4281?project_id=14062
  16. ↑ Yoo, SK & Ito, J (1991) Sequence requirements for protein-primed DNA replication of bacteriophage PRD1. J. Mol. Biol. 218 779-89 PubMed
  17. ↑ Savilahti, H & Bamford, DH (1993) Protein-primed DNA replication: role of inverted terminal repeats in the Escherichia coli bacteriophage PRD1 life cycle. J. Virol. 67 4696-703 PubMed
  18. ↑ 18.0 18.1 18.2 Mindich, L et al. (1982) Isolation of nonsense mutants of lipid-containing bacteriophage PRD1. J. Virol. 44 1013-20 PubMed
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