Phage f1: Difference between revisions
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f1 has a circular, 6407 bp genome of ss-DNA. | f1 has a circular, 6407 bp genome of ss-DNA. | ||
There are 11 genes encoded on the genome; two are overlapping. The genes are generally referred to by numbers or Roman numerals I-X as listed on the [[Gene_List:Phage_f1| f1 Gene]] page. Genes are in the order [[Phage_f1_II:Gene| II]] [[Phage_f1_X:Gene| (X)]], [[Phage_f1_V:Gene| V]], [[Phage_f1_VII:Gene| VII]], [[Phage_f1_IX:Gene| IX]], [[Phage_f1_VIII:Gene| VIII]], [[Phage_f1_III:Gene| III]], [[Phage_f1_VI:Gene| VI]], [[Phage_f1_I:Gene| I]] [[Phage_f1_XI:Gene| (XI)]], [[Phage_f1_IV:Gene| IV]], intergenic region (IG or IGR). <ref name='LIB:Bacteriophages'/> The IGR contains the packing signal (PS) as well as sequences that dictate termination, nicking for replication, and the binding of [[Phage_f1_II:Gene_Product(s)| protein II]] and IHF. <ref name='LIB:Bacteriophages'/> | There are 11 genes encoded on the genome; two are overlapping. The genes are generally referred to by numbers or Roman numerals I-X as listed on the [[Category:Gene_List:Phage_f1| f1 Gene]] page. Genes are in the order [[Phage_f1_II:Gene| II]] [[Phage_f1_X:Gene| (X)]], [[Phage_f1_V:Gene| V]], [[Phage_f1_VII:Gene| VII]], [[Phage_f1_IX:Gene| IX]], [[Phage_f1_VIII:Gene| VIII]], [[Phage_f1_III:Gene| III]], [[Phage_f1_VI:Gene| VI]], [[Phage_f1_I:Gene| I]] [[Phage_f1_XI:Gene| (XI)]], [[Phage_f1_IV:Gene| IV]], intergenic region (IG or IGR). <ref name='LIB:Bacteriophages'/> The IGR contains the packing signal (PS) as well as sequences that dictate termination, nicking for replication, and the binding of [[Phage_f1_II:Gene_Product(s)| protein II]] and IHF. <ref name='LIB:Bacteriophages'/> | ||
== Life cycle == | == Life cycle == | ||
Revision as of 19:50, 29 June 2011
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
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.
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 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 several copies of each pVII and pIX, while 3-5 copies of pIII and pVI seal off the terminally extruded end and give it a bead-like appearance.[1] [2]
Genome Organization
f1 has a circular, 6407 bp genome of ss-DNA.
There are 11 genes encoded on the genome; two are overlapping. The genes are generally referred to by numbers or Roman numerals I-X as listed on the 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] 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. [7] 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. [7] This fastens the viron to the host and allows for the depolymerization of adjacent pVIII, which are distributed into the membrane. [7] It is the degradation of the major coat protein that causes the genome to be released into the cytoplasm of the host.[7]
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] [8] 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 encapsidation it remains partially exposed at the blunt end of the complex. [1]
The phage covering consists of about 2700 copies of the major coat protein encoded by pVIII. [9] 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, remain as integral membrane proteins until needed. [1] Both pI and pXI span the cytoplasmic membrane; together with pIV in the outer membrane they create distinct assembly sites where the membranes are close together. [1]
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) although larger inserts are naturally selected against. [1]
Lysis
This phage does not lyse its host, but can secrete many copies of itself throughout the life of the host cell. The phage are secreted as they are assembled
The host-encoded thiredoxin is required for assembly of nascent phage. The presence of
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]
Excessive copies of the phage genome can be packaged, called "polyphage", but these are due to improper termination of extrusion. [1]
See also
References
See Help:References for how to manage references in EcoliWiki.
- ↑ 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 Edited by Richard Calendar (2006) The Bacteriophages (Oxford University Press, Oxford, NY) ISBN 0-19-514850-9
- ↑ 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
- ↑ 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
- ↑ 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
- ↑ 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
- ↑ Marvin, DA (1998) Filamentous phage structure, infection and assembly. Curr. Opin. Struct. Biol. 8 150-8 PubMed
- ↑ 7.0 7.1 7.2 7.3 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
- ↑ Russel, M et al. (1997) Filamentous phage assembly: variation on a protein export theme. Gene 192 23-32 PubMed
- ↑ 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