Filamentous bacteriophage
Filamentous bacteriophage is a family of viruses (Inoviridae) that infect bacteria. The phages are named for their filamentous shape, a worm-like chain (long, thin and flexible, reminiscent of a length of cooked spaghetti), about 6 nm in diameter and about 1000-2000 nm long.[1][2][3][4][5]The coat of the virion comprises five types of viral protein, which are located during phage assembly in the inner membrane of the host bacteria, and are added to the nascent virion as it extrudes through the membrane. The simplicity of this family makes it an attractive model system to study fundamental aspects of molecular biology, and it has also proven useful as a tool in immunology and nanotechnology.
Filamentous bacteriophages are among the simplest living organisms known, with far fewer genes than the classical tailed bacteriophages studied by the phage group. The family contains 29 defined species, divided between 23 genera.[6][7] However, mining of genomic and metagenomic datasets using a machine learning approach led to the discovery of 10,295 inovirus-like sequences in nearly all bacterial phyla across virtually every ecosystem, indicating that this group of viruses is much more diverse and widespread than originally appreciated.[5]
Three filamentous bacteriophages, fd, f1 and M13, were isolated and characterized by three different research groups in the early 1960s, but they are so similar that they are sometimes grouped under the common name "Ff", which are members of genus Inovirus, as acknowledged by the International Committee on Taxonomy of Viruses (ICTV).[8][9] The molecular structure of Ff phages was determined using a number of physical techniques, especially X-ray fiber diffraction,[2][6] solid-state NMR and cryo-electron microscopy.[10] The structures of the phage capsid and of some other phage proteins are available from the Protein Data Bank.[6] The single-stranded Ff phage DNA runs down the central core of the phage, and is protected by a cylindrical protein coat built from thousands of identical α-helical major coat protein subunits coded by phage gene 8. The gene 8 protein is inserted into the plasma membrane as an early step in phage assembly.[2]Some strains of phage have a "leader sequence" on the gene 8 protein to promote membrane insertion, but others do not seem to need the leader sequence. The two ends of the phage are capped by a few copies of proteins that are important for infection of the host bacteria, and also for assembly of nascent phage particles. These proteins are the products of phage genes 3 and 6 at one end of the phage, and phage genes 7 and 9 at the other end. The fiber diffraction studies identified two structural classes of phage, differing in the details of the arrangement of the gene 8 protein. Class I has a rotation axis relating the gene 8 coat proteins, whereas for Class II this rotation axis is replaced by a helix axis. This technical difference has little noticeable effect on the overall phage structure,but the extent of independent diffraction data is greater for symmetry Class II than for Class I. This assisted the determination of the Class II phage Pf1 structure, and by extension the Class I structure.[2][6]
Structural Class I includes strains fd, f1, M13 of genus Inovirus as well as If1 (of ICTV's species Escherichia virus If1, genus Infulavirus)[11] and IKe (of ICTV's species Salmonella virus IKe, genus Lineavirus),[12] whereas Class II includes strains Pf1 (of ICTV's species Pseudomonas virus Pf1 of genus Primolicivirus),[13] and perhaps also Pf3 (of ICTV's species Pseudomonas virus Pf3 of genus Tertilicivirus),[14] Pf4[15] and PH75 (of NCBI's proposed species Thermus phage PH75, incertae sedis within Inoviridae).[16]
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