Filamentous bacteriophage

Filamentous bacteriophages are among the simplest viruses known, with far fewer genes than the classical tailed bacteriophages studied by the phage group in the mid-20th century. The family contains 29 defined species, divided among 23 genera. 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. The molecular structure of Ff phages was determined using a number of physical techniques, especially X-ray fiber diffraction, and IKe (of ICTV's species Lineavirus IKe, genus Lineavirus), whereas Class II includes strains Pf1 (of ICTV's species Primolicivirus Pf1 of genus Primolicivirus), and perhaps also Pf3 (of ICTV's species Tertilicivirus Pf3 of genus Tertilicivirus), Pf4 and PH75 (of NCBI's proposed species Thermus phage PH75, incertae sedis within Inoviridae). The DNA isolated from fd phage (of genus Inovirus) is single-stranded, and topologically a circle. That is, the DNA single strand extends from one end of the phage particle to the other and then back again to close the circle, although the two strands are not base-paired. This topology was assumed to extend to all other filamentous phages, but it is not the case for phage Pf4, During fd phage assembly, the phage DNA is first packaged into a linear intracellular nucleoprotein complex with many copies of the phage gene 5 replication/assembly protein. The gene 5 protein is then displaced by the gene 8 coat protein as the nascent phage is extruded across the bacterial plasma membrane without killing the bacterial host. The p1 protein of Ff phage (i. e. genus Inovirus), which is required for phage assembly at the membrane, 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 the gene 8 coat protein). 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 the sequence. This assembly mechanism makes this phage a valuable system with which to study transmembrane proteins. is a conserved marker gene that (along with three additional genetic features) was used to automatically detect inovirus sequences. Viral assembly occurs at the inner membrane (in case of Gram-negative bacteria), mediated by a membrane-embedded motor protein complex. was shown in 1987 to integrate into the host bacterial genome, and further such temperate filamentous phages have since been reported, many of which have been implicated in pathogenesis. ==Taxonomy==

The following genera are recognized: • Abaestuovirus • Aclydivirus • Acontivirus • Actovirus • Adiligaturavirus • Affertcholeramvirus • Amentovirus • Anademivirus • Antiavirus • Aspidivirus • Capistrivirus • Catenatiovirus • Circumitovirus • Coriovirus • Fasceasvirus • Femenvirus • Fibrovirus • Galbavirus • Habenivirus • Infulavirus • Inovirus • Itinerivirus • Lineavirus • Lophivirus • Meandervirus • Nigolovirus • Parhipatevirus • Phargevirus • Pilosavirus • Plantarivirus • Porrectionivirus • Primolicivirus • Prolivirus • Propagovirus • Psecadovirus • Pubesvirus • Pythonevirus • Ramphavirus • Restivirus • Reticulivirus • Saetivirus • Sarmentivirus • Scuticavirus • Scytalavirus • Semitavirus • Senectutivirus • Serpentivirus • Siphunculivirus • Staminivirus • Strophivirus • Subteminivirus • Tertilicivirus • Vasivirus • Versovirus • Vicialiavirus • Villovirus • Viscerivirus • Vittavirus • Xiphivirus • Xylivirus Notable members • genus Inovirus aka Ff phages :* species Affertcholeramvirus CTXphi ::* Vibrio phage CTXphi (aka CTXφ bacteriophage) • genus Infulavirus) :* species Infulavirus If1 ::* If1 phage • genus Lineavirus :* species Lineavirus IKe ::* IKe phage • genus Primolicivirus) :* species Primolicivirus Pf1 ::* Pf1 phage • genus Tertilicivirus) :* species Tertilicivirus Pf3 — bacteriophages that infect Pseudomonas aeruginosa ::* Pf3 phage Further notable proposed species are: :* Thermus phage PH75 ::* PH75 phage :* Xanthomonas phage Cf1t (likely misspelled as Cflt) ::* Cf1t phage ==History==

The filamentous particle seen in electron micrographs was initially incorrectly interpreted as contaminating bacterial pilus, but ultrasonic degradation, which breaks flexible filaments roughly in half, inactivated infectivity as predicted for a filamentous bacteriophage morphology. Three filamentous bacteriophages, fd, f1 and M13, were isolated and characterized by three different research groups in the early 1960s. Since these three phages differ by less than 2 percent in their DNA sequences, corresponding to changes in only a few dozen codons in the whole genome, for many purposes they can be considered to be identical. Further independent characterization over the subsequent half-century was shaped by the interests of these research groups and their followers. Genetic studies on M13 using conditional lethal mutants, initiated by David Pratt and colleagues, led to description of phage gene functions. Notably, the protein product of gene 5, which is required for synthesis of progeny single-stranded DNA, is made in large amounts in the infected bacteria, and it binds to the nascent DNA to form a linear intracellular complex. (The simple numbering of genes using Arabic numerals 1,2,3,4... introduced by the Pratt group is sometimes displaced by the practice of using Roman numerals I, II, III, IV... but the gene numbers defined by the two systems are the same). Longer (or shorter) DNA can be included in fd phage, since more (or fewer) protein subunits can be added during assembly as required to protect the DNA, making the phage convenient for genetic studies. The length of the phage is also affected by the positive charge per length on the inside surface of the phage capsid. The genome of fd was one of the first complete genomes to be sequenced. The taxonomy of filamentous bacteriophage was defined by Andre Lwoff and Paul Tournier as family Inophagoviridae, genus I. inophagovirus, species Inophagovirus bacterii (Inos=fiber or filament in Greek), with phage fd (Hoffmann-Berling) as the type species. "Phagovirus" is tautological, and the name of the family was altered to Inoviridae and the type genus to Inovirus. This nomenclature persisted for many decades, and for studies of p8 in membrane mimetic environments. Filamentous bacteriophage engineered to display immunogenic peptides are useful in immunology and wider biological applications. George Smith and Greg Winter used f1 and fd for their work on phage display for which they were awarded a share of the 2018 Nobel Prize in Chemistry. The creation and exploitation of many derivatives of M13 for a wide range of purposes, especially in materials science, has been employed by Angela Belcher and colleagues. Filamentous bacteriophage can promote antibiotic tolerance by forming liquid crystalline domains around bacterial cells. == References ==