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 * Ff phages (for F specific filamentous phages) is a group of phages, including f1, fd and M13, that infect Escherichia coli carrying the F-episome.[1][2][3][4] The virus particle is a flexible filament (worm-like chain) measuring about 6 by 900 nm, with a cylindrical protein tube protecting a single-stranded DNA molecule at its core. The phage has only 11 genes and is one of the simplest organisms known. It has been widely used to study fundamental aspects of molecular biology, for instance membrane protein s.

= Structure =

The Ff phages have a circular ssDNA genome wrapped in a few thousand copies of the major coat protein to give a rod shaped viral particle that is capped on either end with two different sets of proteins. Only one end binds to the F pilus and can inject the DNA into the host cell.

Genetics
contains 9 genes, but produces 11 proteins, thanks to internal translational starts within two genes, pII and pI, which give rise to two additional proteins, pX and pXI, respectively. Phage proteins pII, pV and pX, involved in replication, remain in the cytoplasm, whereas all other proteins are targeted to the membranes

Using a machine learning approach lever- aging a combination of marker gene and genome features, we identified 10,295 inovirus-like sequences from microbial genomes and metagenomes.

The gene encoding p1 has been used as a conserved marker gene, along with three other features specific for inovirus genomes, in an automatic machine-learning approach to identify over 10000 inovirus-like sequences from microbial genomes. roux

Infection
The p3 protein holliger 1999 (PDB entry 1g3p 10.2210/pdb2g3p/pdb) is anchored to one end of the phage particle by the C-terminal domain of p3. Infection of host bacteria involves interaction of two different N-terminal regions of p3 with two different sites of the host bacteria. First, the N2 domain of p3 attaches to the outer tip of the F-pilus, and the pilus retracts into the cell. This retraction may involve depolymerization of the pilus subunit assembly into the cell membrane at the base of the pilus by a reversal of the pili growth and polymerization process. (Craig 2019 Lawley When the tip of the pilus bearing p3 approaches the cell wall, the N1 domain of p3 interacts with the bacterial TolA protein to complete infection and release the genome into the cytoplasm of the host.

use their gene-3-protein (G3P) to infect Escherichia coli cells [1–4]. This protein is located at the tip of the phage and consists of three domains. The C-terminal domainCTanchorsG3Pin the phage coat, thedomain N2 establishes an initial contact with the tip of a pilus, andN1then directs thephageto theC-terminaldomain of the TolA protein (TolA-C), which is the ultimate receptor for filamentous phages (Fig. 1a) [5,6].The TolA binding domains of different filamentous phages show high structural homology, but the pilus binding domains are related neither in sequence nor in structure, presumably because they target different pili. The phages also differ in the arrangement of the domains N1 and N2 of their G3Ps. In the phages IKe and IF1, these domains represent two independent units that are connected by flexible linkers, and thus, the binding sites for the respective pilus and for TolA-C are always accessible [7–9]. In the phagesM13and fd, however,N1 and N2 are firmly associatedmainly via a

network of hydrogen bonds between N1 and the hinge region between the two domains [10–12].Inthis compact conformation (Fig. 1b), the site for the interac- tion of N2 with the F pilus is accessible, but the binding site of N1 for TolA-C is buried at the domain interface, and G3P is auto-inhibited. The initial interaction of the N2 domain with the tip of the F pilus [13,14] thus must be communicated to the domain interface to loosen the interactions between N1, N2, and the hinge region, a prerequisite for exposing the TolA binding site on the N1 domain for the next step of infection [15,16]. The transition to the biologically active state is

accompanied by cis → trans isomerization of Pro213 in the interdomain hinge (Fig. 1b). It arrests G3P in the open, infection-competent form long enough for the N1 domain to interact with its receptor TolA-C and to complete infection [15,16]. The long lifetime of the open conformation results from the local se- quence around Pro213, which decelerates the Pro213 trans → cis re-isomerization [15,17]. During the in vitro refolding of the N1–N2 entity of G3P, called G3P*, the biologically active form with a

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Ff phages need the host cell to be Hfr or F+. When a virion binds to the sex pilus of a host by protein 3 in its beaded end, the pilus retracts and the virus fuses with the host membrane. Several host proteins are involved in this step and the genome of the virus is released into the bacterial cytoplasm.

Replication
After the single-stranded circular viral DNA enters the cytoplasm, it serves as a template for the synthesis of a complementary DNA strand. This synthesis is initiated in the intergenic region of the DNA sequence by host RNA polymerase, which synthesizes a short RNA primer on the infecting DNA as template. The host DNA polymerase III then uses this primer to synthesize the full complementary strand of DNA, yielding a double-stranded circle, sometimes called the replicative form (RF) DNA. The complementary strand of the RF is the transcription template for phage coded proteins, especially p2 and p10, which are necessary for further DNA replication.

The p2 protein cleaves the viral strand of the RF DNA, and host DNA polymerase III synthesizes a new viral strand. The old viral strand is displaced as the new one is synthesized. When a circle is complete, the covalently linked p2 cuts the displaced viral strand at the junction between the old and newly synthesized DNA and re-ligates the two ends and liberates p2. RF replicates by this rolling circle mechanism to generate dozens of copies of the RF.

When the concentration of phage proteins has increased, new viral strands are coated by the replication/assembly protein p5 rather than by the complementary DNA strands, The p5 also inhibits translation of p2, so that progeny viral ssDNA production and packaging are in synchrony. The ssDNA-p5 complex interacts with the membrane-bound p1/p11/p4 proteins which contribute to the extrusion process, and also with the p7 and p9 proteins which form the tip of the progeny virus.

pV has an additional regulatory role – it inhibits translation of pII (Michel and Zinder, 1989). This regulatory loop serves to coordinate ssDNA production and packaging. The packaging or morphogenetic signal targets the

ssDNA-pV complex to the pI/pXI/pIV phage export complex and assists the minor proteins pVII and pIX in identifying phage ssDNA genomes so that they can be packaged into virions and exported (Russel and Model, 1989). Only the packaging signal on the positive strand is recognized and packaged (Zinder and Horiuchi, 1985). It has been noted, however, that the export system packages ssDNA of Ff mutants that do not contain the packaging signal as well as unrelated plasmid ssDNA, albeit at a low efficiency (Russel and Model, 1989). In Ff filamentous bacteriophage, some truncated

virions are produced, often after about 40 passages of the phage through host cells in the absence of clonal (plaque) purification, when genomes containing spontaneous duplications of the replication origin tend to appear in the culture (La Farina et al., 1987). In these spontaneous double-origin genomes, (+) strand replication is initiated at the origin 1 (ori1); when the replication fork reaches the next positive origin 2 (ori2) the termination signal is recognized by pII, which makes another cut and then ligates the two ends of the (+) strand, to create a small genome spanning the segment between ori1 and ori2. Given that virion length is determined by the size of packaged ssDNA, the resulting virions are relatively short. This small replicating segment interferes with full-length genome replication and packaging, the short virions becoming a significant fraction of the phage progeny. This property has been used to engineer a “microphage”-producing template – a plasmid containing the packaging signal flanked by two

Filamentous

The single stranded DNA of the virus is converted into double stranded DNA by the host machinery. This form is called the replicative form (RF). The strand which came from the virus (VS) is nicked by the viral protein p2 (pII).[6] Host DNA replication machinery then replicates the VS in a rolling circle form of replication by extending the 3' end of the nick, pushing out the 5' end as a single strand. P2 chops off the strand each time its extension completes a full circle and ligates the single stranded copy into a circle.[6] These ssDNA circles are converted to dsDNA like the original viral genome and the RFs accumulate in the cell. The RFs are transcribed and viral proteins accumulate. The RFs are passed on indefinitely to the daughter cells as plasmids.

Assembly and extrusion
Infection does not kill the host bacteria, in contrast to most other families of phage. Progeny phage are assembled as they extrude through the membrane of growing bacteria, probably at adhesion sites joining inner and outer membranes. The five phage proteins that form the coat of the completed phage enter the inner membrane; for p8 and p3, N-terminal leader sequences (later removed) help the proteins to enter the bacterial membrane, with their N-termini directed away from the cytoplasm towards the periplasm. Three other phage membrane proteins that are not present in the phage, p1, p11, and p4, are also involved in assembly. Replication of RF DNA is converted to production of phage ssDNA by coating of the DNA with p5 to form an elongated p5/DNA complex, which then interacts with the membrane-bound phage proteins. The extrusion process picks up the p7 and p9 proteins which form the outer tip of the progeny phage. As the p5 is stripped off the DNA, the progeny DNA is extruded across the membrane and wrapped in a helical casing of p8, to which p3 and p6 are added at the end of assembly. The p4 protein may form an extrusion pore in the outer membrane. straus

Interaction of the double-stranded packaging DNA signal with the p1-thioredoxin complex at the host inner membrane triggers the formation of a pore. The p1 protein, which provides the energy needed to drive phage assembly, has a membrane-spanning hydrophobic domain with the N-terminal portion in the cytoplasm and the C-terminal portion in the periplasm (the reverse of the orientation of p8). Adjacent to the cytoplasmic side of the membrane-spanning domain is a 13- residue sequence of p1 having a pattern of basic residues closely matching the pattern of basic residues near the C terminus of p8, but inverted with respect to that sequence.(Rapoza and Webster, 1995

Intermediate assemblies of p8 can be generated by treating the phage with chloroform (Manning and Griffith 1985; Stopar et al. 1998). The helical content of p8 in these intermediate forms is similar to that in the phage, suggesting that the structural change of the assembly may involve just a sliding of the shingled p8 subunits with respect to their neighbours in the assembly.