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Phage f1

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Bacteriophage f1 is structurally classified as a class I filamentous phage, and is closely related to the other Ff phages, Phage M13 and phage fd. [1] [2]

The full sequence is available from NCBI at GenBank: J02448.1

Ambox notice.png Phage f1 can refer to a number of different phages. This page is about phage f1, a ssDNA filamentous phage. However, phage f1 is also the name used for a ssRNA icosahedral phage and phage F1 is another ssDNA phage.

Contents

Morphology

Phage f1 is a filamentous (rod-shaped) ssDNA phage, with a molecular mass of about 1.6x107 Da; by weight it is 11.3 percent DNA. [3] [4] The flexible phages are about 8500 Å (850 nm) long, and depending on the staining technique, appear to be 43 or 63 Å wide. [4] The thousands of identical major coat proteins that make up the sheath are slightly curved, enlongated proteins about 70 Å by 10 Å and are arranged in an α-helix. [5] [6] These sheath proteins slightly overlap and are oriented just slightly off of perpendicular (20°) to the length of the filament; they are interdigitated and slope radially (with a 5-fold rotation axis and 2-fold helical axis) to form a fishscale-like coating for the DNA core. [1] [5]

The ends of the filament are sealed with protein caps. The end that is extruded first appears blunt and contains 3-5 copies of each pVII and pIX, while about 5 copies each of pIII and pVI seal off the terminally extruded end and give it a bead-like appearance.[1] [2]

Genome Organization

J02448 on NCBI




f1 has a circular, 6407 bp genome of ss-DNA.

There are 11 genes encoded on the genome; two are overlapping in-frame genes. Five of the encoded proteins make up the viron, three are needed for synthesis and the rest are for assembly. [7] The genes are generally referred to by Roman numerals I-XI as listed on the Phage f1 page. Genes are in the order II (X), V, VII, IX, VIII, III, VI, I (XI), IV, intergenic region (IG or IGR). [1] The IGR contains the packing signal (PS) as well as sequences that dictate termination, nicking for replication, and the binding of protein II and IHF. [1]

Life cycle

Adsorption and Injection

f1 is male specific; it only infects Hfr or F+ strains of E. coli. [4] (See Russel et al. 1988 for a study showing that filamentous particles with a plasmid and phage DNA are sufficient for infecting F- bacteria at a low frequency of 10E-6, but requires several host proteins.)

The host protein tolA, along with tolQ and tolR, are required for infection and depolymerization of the coat proteins of the phage. [1] [2] The N2 domain of pIII binds to the primary receptor, the tip of the F pilus, and retraction of the pilus by an unknown mechanism brings the N1 domain of pIII close enough to the membrane to bind the coreceptor tolA.[2]

The removal of the cap proteins and release of the ssDNA into the cytoplasm are both mediated by the interactions of tolA and pIII. [8] At least one pIII undergoes a conformational change in the C domain as a result of the N1/tolA interaction; the hydrophobic portion of pIII is revealed and inserts itself into the inner membrane. [8] This fastens the viron to the host and allows for the depolymerization of adjacent pVIII, which are distributed into the membrane. [8] It is the degradation of the major coat protein that causes the genome to be released into the cytoplasm of the host.[8]

DNA replication

The ssDNA genome is replicated and translated with host enzymes after it is inserted into the cytoplasm. RNA polymerase creates a primer on the existing (+) strand in the IGR region due to the strong promoter-like signals from -35 and -10 motifs on two hairpin sequences that are stronger than host promoter signals. [1] Host DNA polymerase III replicates the remainder of the strand to create a dsDNA product that is further processed by host gyrase to form a supercoiled RF template used for replication. [1]

Phage pII specifically cuts the (+) strand at the origin, and the genome is replicated from 3' end of the template (-) strand using rolling circle replication, with host Rep helicase displacing the (+) strand. [1] The pII protein is also necessary for ligation of the newly isolated (+) strand, which is replicated in the same manner as the original ssDNA genome. [1] Host enzymes are also necessary to translate the phage proteins.

Phage proteins can be detected in the supernatant about 10 minutes after infection (37°). [1]

Packaging

Exponential accumulation of the phage proteins, including pV, allows for the formation of a DNA- pV complex, hundreds of which can form per host. [1] [2] The complexes prevent further copies of the complement strand from being made, and also "pre-package" and stabilize the ssDNA into an almost linear form.[1] [2] About 1500 copies of pV, which are dimers at physiological salt concentrations, form a flexible, semi-enclosed left-handed helix about 8x800-900 nm that encapsulate the DNA. [1] [2] [7] The ssDNA does not interact with itself inside the capsule, and remains untwisted and unpaired except for the extremely stable packing signal.[1] The PS exists as an imperfect hairpin and is responsible for the attachment and orientation of the genome in the phage. [1] Proper packing can be accomplished if and only if the PS is present; even after the genome has been covered it remains partially exposed at the blunt end of the complex. [1]

Lysis

This phage does not lyse its host, but can secrete many copies of itself throughout the life of the host cell. The cell can continue to divide even while infected, with minimal affect on the cell metabolism. [1] [9] The phage are secreted as they are assembled, and once the pV-DNA complex is formed all further assembly and secretion steps take place in or at a membrane. [7] The proteins depolymerized upon phage entry can be reused for the packaging of new phage, and as with newly synthesized coat proteins pIII, pVI, pVII, pVIII and pIX, the proteins remain as integral membrane proteins until needed. [1]

Both pI and pXI span the cytoplasmic membrane; together with the outer membrane protein pIV they create distinct assembly sites (adhesion zones) where the membranes are close together. [1] It is possible that pIV multimers form controlled channels for the export of nascent phage, although the exact mechanism for phage exit is unclear. [7] The PS is likely recognized by pI; this protein is also thought to bind thioredoxin and promote the addition of pVIII to the elongating phage. [7]

The host-encoded thioredoxin is the only known host protein required for assembly of nascent phage and likely confers processivity. [7] [1] The presence of a properly presented ssDNA in an adhesion zone with thioredoxin, major coat protein, and the minor coat proteins pXI and pI allows for the elongation and secretion of phages. [1]. The phage is enlongated by continually removing pV dimers and replacing them with the major coat protein. The phage coat consists of about 2700 copies of the major coat protein encoded by pVIII. [10]

The end of the DNA signals the cell to add pVI and pIII, which are likely already associated with the major coat protein. A modified 132-residue form of pIII is required for stabilization of the phage, while a shorter 93-residue (also the C-terminal portion) is sufficient for release and the last 83-residue portion of the C-terminal is capable of binding pVI. [1] [3] As with most filamentous phages, there is no defined limit on the amount of DNA that can be packaged into the phage coat (contrast to phages with set capsid size, such as phage λ). [1] Excessive copies of the phage genome can be packaged, called "polyphage"; although these are due to improper termination of extrusion about 5% of the phage produced in the presence of termination signals are twice the normal length. [1] Even larger inserts are naturally selected against. [1] The non-terminated phage will remain anchored to the host, and attachment of another pV-DNA complex will continue the enlongation process.[1] The PS site is only needed to initiate elongation, not for the attachment of additional genomes.[1]

Another domain of pIII is responsible for defects in the outer membrane, which result in the seepage of periplasmic contents and increase the host's susceptibility to detergents. [1]


Phage can be assembled and released at a very high rate, with up to 1000 progeny released within an hour of infection of the host. [11]

See also

References

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  1. 1.00 1.01 1.02 1.03 1.04 1.05 1.06 1.07 1.08 1.09 1.10 1.11 1.12 1.13 1.14 1.15 1.16 1.17 1.18 1.19 1.20 1.21 1.22 1.23 1.24 1.25 1.26 1.27 1.28 Edited by Richard Calendar (2006) The Bacteriophages (Oxford University Press, Oxford, NY) ISBN 0-19-514850-9
  2. 2.0 2.1 2.2 2.3 2.4 2.5 2.6 Lubkowski, J et al. (1999) Filamentous phage infection: crystal structure of g3p in complex with its coreceptor, the C-terminal domain of TolA. Structure 7 711-22 PubMed EcoliWiki page
  3. 3.0 3.1 Endemann, H & Model, P (1995) Location of filamentous phage minor coat proteins in phage and in infected cells. J. Mol. Biol. 250 496-506 PubMed EcoliWiki page
  4. 4.0 4.1 4.2 ZINDER, ND et al. (1963) F1, A ROD-SHAPED MALE-SPECIFIC BACTERIOPHAGE THAT CONTAINS DNA. Virology 20 638-40 PubMed EcoliWiki page
  5. 5.0 5.1 Straus, SK et al. (2011) Consensus structure of Pf1 filamentous bacteriophage from X-ray fibre diffraction and solid-state NMR. Eur. Biophys. J. 40 221-34 PubMed EcoliWiki page
  6. Marvin, DA (1998) Filamentous phage structure, infection and assembly. Curr. Opin. Struct. Biol. 8 150-8 PubMed EcoliWiki page
  7. 7.0 7.1 7.2 7.3 7.4 7.5 Russel, M et al. (1997) Filamentous phage assembly: variation on a protein export theme. Gene 192 23-32 PubMed EcoliWiki page
  8. 8.0 8.1 8.2 8.3 Bennett, NJ & Rakonjac, J (2006) Unlocking of the filamentous bacteriophage virion during infection is mediated by the C domain of pIII. J. Mol. Biol. 356 266-73 PubMed EcoliWiki page
  9. Marvin, DA & Hohn, B (1969) Filamentous bacterial viruses. Bacteriol Rev 33 172-209 PubMed EcoliWiki page
  10. Haigh, NG & Webster, RE (1998) The major coat protein of filamentous bacteriophage f1 specifically pairs in the bacterial cytoplasmic membrane. J. Mol. Biol. 279 19-29 PubMed EcoliWiki page
  11. Russel, M (1991) Filamentous phage assembly. Mol. Microbiol. 5 1607-13 PubMed EcoliWiki page