Filamentous bacteriophages are a family ofviruses (Inoviridae) that infectbacteria, orbacteriophages. They are named for their filamentous shape, aworm-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] This distinctive shape reflects theirmethod of replication: the coat of the virion comprises five types of viral protein, which are located in the inner membrane of the host bacterium during phage assembly, and these proteins are added to the nascent virion's DNA as it is extruded through the membrane. The simplicity of filamentous phages makes them an appealingmodel organism for research inmolecular biology, and they have also shown promise as tools innanotechnology andimmunology.
Assembled major coat protein subunits in Ff (fd, f1, M13) filamentous bacteriophage (genusInovirus), exploded view.Filamentous phage virion--schematic views
Filamentous bacteriophages are among the simplest living organisms known, with far fewer genes than the classicaltailed bacteriophages studied by thephage group in the mid-20th century. The family contains 29 defined species, divided among 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 the genusInovirus, as acknowledged by theInternational Committee on Taxonomy of Viruses (ICTV).[8][9] The molecular structure of Ff phages was determined using a number of physical techniques, especially X-rayfiber diffraction,[2][6]solid-state NMR andcryo-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 genusInovirus as well as If1 (of ICTV's speciesEscherichia virus If1, genusInfulavirus)[11] and IKe (of ICTV's speciesSalmonella virus IKe, genusLineavirus),[12] whereas Class II includes strains Pf1 (of ICTV's speciesPseudomonas virus Pf1 of genusPrimolicivirus),[13] and perhaps also Pf3 (of ICTV's speciesPseudomonas virus Pf3 of genusTertilicivirus),[14] Pf4[15] and PH75 (of NCBI's proposed speciesThermus phage PH75,incertae sedis withinInoviridae).[16]
The DNA isolated from fd phage (of genusInovirus) 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,[15] for which the DNA in the phage is single-stranded but topologically linear, not circular.[10] 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.[17][18][2][19] This protein also binds with high affinity toG-quadruplex structures (although they are not present in the phage DNA) and to similar hairpin structures in phage DNA.[20]
The p1 protein of Ff phage (i. e. genusInovirus), 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 studytransmembrane proteins.[2][21][4] Gene 1, coding for an ATPase,[22] is a conserved marker gene that (along with three additional genetic features) was used to automatically detect inovirus sequences.[5]
Viral replication is cytoplasmic. Entry into the host cell is achieved bypilus-mediated adsorption into the host cell. Replication follows the ssDNA rolling circle model. DNA-templated transcription is the method of transcription. The virus exits the host cell by viral extrusion.[23] Viral assembly occurs at the inner membrane (in case of Gram-negative bacteria), mediated by a membrane-embedded motor protein complex.[23] This multimeric assembly complex, including p1 encoded by gene 1 (referred to as ZOT, zonula occludens toxin by researchers on Vibrio cholerae phage CTXΦ) is an ATPase containing functional and essentialWalker motifs[22] that are thought to mediate the hydrolysis of ATP providing the energy for the assembly of the phage filament. Filamentous phage Cf1t fromXanthomonas campestris (of NCBI's proposed speciesXanthomonas phage Cf1t,incertae sedis withinInoviridae, likely misspelled as Cflt),[24]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.[1]
On base ofmetagenomical data, the family has been proposed to be split into new familiesAmplinoviridae,Protoinoviridae,Photinoviridae,Vespertilinoviridae,Densinoviridae, andPaulinoviridae, all within orderTubulavirales.[28]
The filamentous particle seen in electron micrographs was initially incorrectly interpreted as contaminating bacterialpilus, but ultrasonic degradation, which breaks flexible filaments roughly in half,[30] inactivated infectivity as predicted for a filamentous bacteriophage morphology.[31] 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.[32] Further independent characterization over the subsequent half-century was shaped by the interests of these research groups and their followers.[2]
Filamentous phages, unlike most other phages, are continually extruded through the bacterial membrane without killing the host.[19] Genetic studies on M13 using conditional lethal mutants, initiated by David Pratt and colleagues, led to description of phage gene functions.[33][34] 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,[35][36][37] and it binds to the nascent DNA to form a linear intracellular complex.[17] (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.[38][39] The length of the phage is also affected by the positive charge per length on the inside surface of the phage capsid.[40] The genome of fd was one of the first complete genomes to be sequenced.[41]
The taxonomy of filamentous bacteriophage was defined byAndre 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.[42][43] "Phagovirus" istautological, and the name of the family was altered toInoviridae and the type genus toInovirus. This nomenclature persisted for many decades,[9] although the definition of fd as type species was replaced as M13 became more widely used for genetic manipulation,[44][45] and for studies of p8 in membrane mimetic environments.[2] The number of known filamentous bacteriophages has multiplied many-fold by using a machine-learning approach, and it has been suggested that "the former Inoviridae family should be reclassified as an order, provisionally divided into 6 candidate families and 212 candidate subfamilies".[5] Phages fd, f1, M13 and other related phages areFf phages, forF specific (they infectEscherichia coli carrying theF-episome)filamentous phages, using the concept of vernacular name.[46]
Filamentous bacteriophage engineered to displayimmunogenic peptides are useful in immunology and wider biological applications.[47][48][49][50] George Smith and Greg Winter used f1 and fd for their work onphage 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 byAngela Belcher and colleagues.[50][51][52][53] Filamentous bacteriophage can promote antibiotic tolerance by forming liquid crystalline domains[54] around bacterial cells.[55][10]
^abcdefghStraus SK, Bo HE (2018). "Filamentous Bacteriophage Proteins and Assembly". In Bhella JR, Harris D (eds.).Virus Protein and Nucleoprotein Complexes. Subcellular Biochemistry. Vol. 88. Springer Singapore. pp. 261–279.doi:10.1007/978-981-10-8456-0_12.ISBN978-981-10-8455-3.PMID29900501.
^abRakonjac J, Russel M, Khanum S, Brooke SJ, Rajič M (2017). "Filamentous Phage: Structure and Biology". In Lim TS (ed.).Recombinant Antibodies for Infectious Diseases. Advances in Experimental Medicine and Biology. Vol. 1053. Springer International Publishing. pp. 1–20.doi:10.1007/978-3-319-72077-7_1.ISBN978-3-319-72076-0.PMID29549632.
^abPratt D, Laws P, Griffith J (February 1974). "Complex of bacteriophage M13 single-stranded DNA and gene 5 protein".Journal of Molecular Biology.82 (4):425–39.doi:10.1016/0022-2836(74)90239-3.PMID4594145.
^Gray CW (July 1989). "Three-dimensional structure of complexes of single-stranded DNA-binding proteins with DNA. IKe and fd gene 5 proteins form left-handed helices with single-stranded DNA".Journal of Molecular Biology.208 (1):57–64.doi:10.1016/0022-2836(89)90087-9.PMID2671388.
^abHoffmann Berling H, Maze R (March 1964). "Release of male-specific bacteriophages from surviving host bacteria".Virology.22 (3):305–13.doi:10.1016/0042-6822(64)90021-2.PMID14127828.
^Wen JD, Gray DM (March 2004). "Ff gene 5 single-stranded DNA-binding protein assembles on nucleotides constrained by a DNA hairpin".Biochemistry.43 (9):2622–34.doi:10.1021/bi030177g.PMID14992600.
^Rapoza, M.P.; Webster, R. L. (1995). "The Products of Gene I and the Overlapping in-Frame Gene XI are Required for Filamentous Phage Assembly".J. Mol. Biol.248 (3):627–638.doi:10.1006/jmbi.1995.0247.PMID7752229.
^Pratt D, Tzagoloff H, Erdahl WS (November 1966). "Conditional lethal mutants of the small filamentous coliphage M13. I. Isolation, complementation, cell killing, time of cistron action".Virology.30 (3):397–410.doi:10.1016/0042-6822(66)90118-8.PMID5921643.
^Pratt D, Tzagoloff H, Beaudoin J (September 1969). "Conditional lethal mutants of the small filamentous coliphage M13. II. Two genes for coat proteins".Virology.39 (1):42–53.doi:10.1016/0042-6822(69)90346-8.PMID5807970.
^Pratt D, Erdahl WS (October 1968). "Genetic control of bacteriophage M13 DNA synthesis".Journal of Molecular Biology.37 (1):181–200.doi:10.1016/0022-2836(68)90082-X.PMID4939035.
^Alberts B, Frey L, Delius H (July 1972). "Isolation and characterization of gene 5 protein of filamentous bacterial viruses".Journal of Molecular Biology.68 (1):139–52.doi:10.1016/0022-2836(72)90269-0.PMID4115107.
^Herrmann R, Neugebauer K, Zentgraf H, Schaller H (February 1978). "Transposition of a DNA sequence determining kanamycin resistance into the single-stranded genome of bacteriophage fd".Molecular & General Genetics.159 (2):171–8.doi:10.1007/bf00270890.PMID345091.S2CID22923713.
^Greenwood J, Hunter GJ, Perham RN (January 1991). "Regulation of filamentous bacteriophage length by modification of electrostatic interactions between coat protein and DNA".Journal of Molecular Biology.217 (2):223–7.doi:10.1016/0022-2836(91)90534-d.PMID1992159.
^Casey JP, Barbero RJ, Heldman N, Belcher AM (November 2014). "Versatile de novo enzyme activity in capsid proteins from an engineered M13 bacteriophage library".Journal of the American Chemical Society.136 (47):16508–14.doi:10.1021/ja506346f.PMID25343220.
^Oh D, Qi J, Han B, Zhang G, Carney TJ, Ohmura J, et al. (August 2014). "M13 virus-directed synthesis of nanostructured metal oxides for lithium-oxygen batteries".Nano Letters.14 (8):4837–45.Bibcode:2014NanoL..14.4837O.doi:10.1021/nl502078m.PMID25058851.
^Dorval Courchesne NM, Klug MT, Huang KJ, Weidman MC, Cantú VJ, Chen PY, et al. (June 2015). "Constructing Multifunctional Virus-Templated Nanoporous Composites for Thin Film Solar Cells: Contributions of Morphology and Optics to Photocurrent Generation".The Journal of Physical Chemistry C.119 (25):13987–4000.doi:10.1021/acs.jpcc.5b00295.hdl:1721.1/102981.ISSN1932-7447.
