F1 phage
Encyclopedia
Bacteriophage
f1 is structurally classified as a class I filamentous phage
, and is closely related to the other Ff phages, such as M13 and phage fd.
In the following page, genes will be written in italics and their associated proteins in Roman.
of about 1.6x107 Da; by weight it is 11.3 percent DNA
. The flexible phages are about 8500 Å (850 nm) long and 43 or 63 Å wide. The thousands of identical major coat proteins that make up the sheath are arranged in a fishcale-like α-helix.
The ends of the filament are sealed with protein caps; the blunt end contains 3-5 copies of each VII and IX, while the terminally extruded bead-like end contains about 5 copies each of III and VI.
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. The genes are generally referred to by Roman numerals I-XI, and are in the order II(X), V, VII, IX, VIII, III, VI, I(XI), IV, intergenic region (IG or IGR). The IGR contains the packing signal (PS) as well as sequences that dictate termination, nicking for replication, and the binding of II and IHF.
Several host proteins are required for infection and depolymerization
of the coat proteins of the phage.
A domain of III binds to the primary receptor, the tip of the F pilus, and retraction of the pilus by an unknown mechanism brings another domain of III close enough to the membrane to bind the coreceptor, host tolA.
The removal of the cap proteins and release of the ssDNA into the cytoplasm
are both mediated by the interactions of tolA and III.
A hydrophobic
portion of III inserts itself into the inner membrane, fastening the phage particle to the host and distributing the coat proteins into the host membrane. It is the degradation of the major coat protein that causes the genome to be released into the cytoplasm of the host.
s after it is inserted into the cytoplasm. RNA
polymerase
, DNA polymerase III, and host gyrase form a supercoiled RF template used for replication.
Phage II specifically cuts the (+) strand at the origin, and host Rep helicase
aids rolling circle replication. II is necessary for ligation of the newly isolated (+) strand, and more host enzymes are necessary for translation.
Phage proteins can be detected in the supernatant about 10 minutes after infection (37°).
The ssDNA does not interact with itself inside the capsule, and remains untwisted and unpaired except for the extremely stable packing signal. The PS exists as an imperfect hairpin and is responsible for the attachment and orientation of the genome in the phage. 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.
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, and cell metabolism is minimally affected by the phage.
The phage are secreted as they are assembled, and once the DNA-V complex is formed all further assembly and secretion steps take place in or at a membrane. The proteins depolymerized upon phage entry can be reused for the packaging of new phage, and as with newly synthesized coat proteins, the proteins remain as integral membrane proteins until needed.
The host-encoded thioredoxin
is the only known host protein required for assembly of nascent phage and likely confers processivity
. The presence of a properly presented ssDNA in an adhesion zone with thioredoxin and the coat proteins allows for the elongation and secretion of phages. The phage is enlongated by continually removing dimer
s of V and replacing them with the major coat protein. The phage coat consists of about 2700 copies of VIII. The end of the DNA signals the cell to add the end cap proteins, which are likely already associated with VIII.
As with most filamentous phages, there is no defined limit on the amount of DNA that can be packaged into the phage coat. 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. Even larger inserts are naturally selected against. The non-terminated phage will remain anchored to the host, and attachment of another V-DNA complex will continue the enlongation process. The PS site is only needed to initiate elongation, not for the attachment of additional genomes.
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.
Bacteriophage
A bacteriophage is any one of a number of viruses that infect bacteria. They do this by injecting genetic material, which they carry enclosed in an outer protein capsid...
f1 is structurally classified as a class I filamentous phage
Filamentous phage
A filamentous phage is a type of bacteriophage shaped like a rod filament. Filamentous phages usually contain a genome of single-stranded DNA and infect Gram-negative bacteria.-Types of filamentous phage:*Ff phages - these infect E...
, and is closely related to the other Ff phages, such as M13 and phage fd.
In the following page, genes will be written in italics and their associated proteins in Roman.
Morphology
Phage f1 is a filamentous (rod-shaped) ssDNA phage, with a molecular massMolecular mass
The molecular mass of a substance is the mass of one molecule of that substance, in unified atomic mass unit u...
of about 1.6x107 Da; by weight it is 11.3 percent DNA
DNA
Deoxyribonucleic acid is a nucleic acid that contains the genetic instructions used in the development and functioning of all known living organisms . The DNA segments that carry this genetic information are called genes, but other DNA sequences have structural purposes, or are involved in...
. The flexible phages are about 8500 Å (850 nm) long and 43 or 63 Å wide. The thousands of identical major coat proteins that make up the sheath are arranged in a fishcale-like α-helix.
The ends of the filament are sealed with protein caps; the blunt end contains 3-5 copies of each VII and IX, while the terminally extruded bead-like end contains about 5 copies each of III and VI.
Genome Organization
f1 has a circular, 6407 bp genomeGenome
In modern molecular biology and genetics, the genome is the entirety of an organism's hereditary information. It is encoded either in DNA or, for many types of virus, in RNA. The genome includes both the genes and the non-coding sequences of the DNA/RNA....
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
Viron
Viron may refer to:*Viron, a Finnish word for "Estonia's" or "of Estonia"*Viron, a Greek form of Byron and an alternative form of the city of Vyronas in suburban Athens, Greece...
, three are needed for synthesis and the rest are for assembly. The genes are generally referred to by Roman numerals I-XI, and are in the order II(X), V, VII, IX, VIII, III, VI, I(XI), IV, intergenic region (IG or IGR). The IGR contains the packing signal (PS) as well as sequences that dictate termination, nicking for replication, and the binding of II and IHF.
Adsorption and Injection
f1 is male specific; it only infects Hfr or F+ strains of E. coli.Several host proteins are required for infection and depolymerization
Depolymerization
Depolymerization is the process of converting a polymer into a monomer or a mixture of monomers.Thioglycolysis, thiolysis and phloroglucinolysis are reactions used to study condensed tannins by means of their depolymerisation. Thioglycolysis is also used to study lignin....
of the coat proteins of the phage.
A domain of III binds to the primary receptor, the tip of the F pilus, and retraction of the pilus by an unknown mechanism brings another domain of III close enough to the membrane to bind the coreceptor, host tolA.
The removal of the cap proteins and release of the ssDNA into the cytoplasm
Cytoplasm
The cytoplasm is a small gel-like substance residing between the cell membrane holding all the cell's internal sub-structures , except for the nucleus. All the contents of the cells of prokaryote organisms are contained within the cytoplasm...
are both mediated by the interactions of tolA and III.
A hydrophobic
Hydrophobia
Hydrophobia or hydrophobe may refer to:* Rabies, especially a set of symptoms of the later stages of an infection, in which the victim has difficulty swallowing, shows panic when presented with liquids to drink, and cannot quench his or her thirst....
portion of III inserts itself into the inner membrane, fastening the phage particle to the host and distributing the coat proteins into the host membrane. It is the degradation of the major coat protein that causes the genome to be released into the cytoplasm of the host.
DNA replication
The ssDNA genome is replicated and translated with host enzymeEnzyme
Enzymes are proteins that catalyze chemical reactions. In enzymatic reactions, the molecules at the beginning of the process, called substrates, are converted into different molecules, called products. Almost all chemical reactions in a biological cell need enzymes in order to occur at rates...
s after it is inserted into the cytoplasm. RNA
RNA
Ribonucleic acid , or RNA, is one of the three major macromolecules that are essential for all known forms of life....
polymerase
Polymerase
A polymerase is an enzyme whose central function is associated with polymers of nucleic acids such as RNA and DNA.The primary function of a polymerase is the polymerization of new DNA or RNA against an existing DNA or RNA template in the processes of replication and transcription...
, DNA polymerase III, and host gyrase form a supercoiled RF template used for replication.
Phage II specifically cuts the (+) strand at the origin, and host Rep helicase
Helicase
Helicases are a class of enzymes vital to all living organisms. They are motor proteins that move directionally along a nucleic acid phosphodiester backbone, separating two annealed nucleic acid strands using energy derived from ATP hydrolysis.-Function:Many cellular processes Helicases are a...
aids rolling circle replication. II is necessary for ligation of the newly isolated (+) strand, and more host enzymes are necessary for translation.
Phage proteins can be detected in the supernatant about 10 minutes after infection (37°).
Packaging
DNA-V complexes form in the hundreds and prevent further copies of the complement strand from being made while also "pre-packaging" and stabilize the ssDNA into an almost linear form. About 1500 copies of V form a flexible, semi-enclosed left-handed helix that encapsulate the DNA.The ssDNA does not interact with itself inside the capsule, and remains untwisted and unpaired except for the extremely stable packing signal. The PS exists as an imperfect hairpin and is responsible for the attachment and orientation of the genome in the phage. 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.
Lysis
This phage does not lyseLysis
Lysis refers to the breaking down of a cell, often by viral, enzymic, or osmotic mechanisms that compromise its integrity. A fluid containing the contents of lysed cells is called a "lysate"....
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, and cell metabolism is minimally affected by the phage.
The phage are secreted as they are assembled, and once the DNA-V complex is formed all further assembly and secretion steps take place in or at a membrane. The proteins depolymerized upon phage entry can be reused for the packaging of new phage, and as with newly synthesized coat proteins, the proteins remain as integral membrane proteins until needed.
The host-encoded thioredoxin
Thioredoxin
Thioredoxin is a class of small redox proteins known to be present in all organisms. It plays a role in many important biological processes. In humans, it is encoded by the TXN gene. Loss-of-function mutation of either of the two human thioredoxin genes is lethal at the four-cell stage of the...
is the only known host protein required for assembly of nascent phage and likely confers processivity
Processivity
In molecular biology, processivity is a measure of the average number of nucleotides added by a DNA polymerase enzyme per association/disassociation with the template. DNA polymerases associated with DNA replication tend to be highly processive, while those associated with DNA repair tend to have...
. The presence of a properly presented ssDNA in an adhesion zone with thioredoxin and the coat proteins allows for the elongation and secretion of phages. The phage is enlongated by continually removing dimer
Dimer
A dimer is a chemical entity consisting of two structurally similar subunits called monomers joined by bonds that can be either strong or weak.- Organic chemistry :...
s of V and replacing them with the major coat protein. The phage coat consists of about 2700 copies of VIII. The end of the DNA signals the cell to add the end cap proteins, which are likely already associated with VIII.
As with most filamentous phages, there is no defined limit on the amount of DNA that can be packaged into the phage coat. Excessive copies of the phage genome can be packaged, called "polyphage
Polyphage
For the dietary behaviour term, see polyphagy.Polyphage are genomic multimers of bacteriophage all encapsulated, one after the other, within the same set of coat proteins....
"; 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. Even larger inserts are naturally selected against. The non-terminated phage will remain anchored to the host, and attachment of another V-DNA complex will continue the enlongation process. The PS site is only needed to initiate elongation, not for the attachment of additional genomes.
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.