Microviridae

Microviridae is a family of bacteriophages with a single-stranded DNA genome. The name of this family is derived from the ancient Greek word μικρός (mikrós), meaning "small".[1][2] This refers to the size of their genomes, which are among the smallest of the DNA viruses. Enterobacteria, intracellular parasitic bacteria, and spiroplasma serve as natural hosts. There are currently 21 species in this family, divided among six genera and two subfamilies.[3][4]

Microviridae
Virus classification
(unranked):	Virus
Realm:	Monodnaviria
Kingdom:	Sangervirae
Phylum:	Phixviricota
Class:	Malgrandaviricetes
Order:	Petitvirales
Family:	Microviridae
Subfamilies and genera
Subfamily:Bullavirinae Alphatrevirus Gequatrovirus Sinsheimervirus Subfamily: Gokushovirinae Bdellomicrovirus Chlamydiamicrovirus Spiromicrovirus

Virology

The virons are non-enveloped, round with an icosahedral symmetry (T = 1). They have a diameter between 25–27 nanometers and lack tails. Each viron has 60 copies each of the F, G, and J proteins and 12 copies of the H protein. They have 12 pentagonal trumpet-shaped pentamers (~7.1 nm wide × 3.8 nm high), each of which composed of 5 copies of G and one of the H protein.

Viruses in this family replicate their genomes via a rolling circle mechanism and encode dedicated RCR initiation proteins.[5][6]

Although the majority of species in this family have lytic life cycles, a few may have temperate life cycles.[7]

Genome

The 5386 bp genome of bacteriophage ΦX174 showing the 11 genes and reading frame overlaps

The genome sizes range from 4.5–6kb and is circular. It encodes 11 genes (in order: A, A*, B, C, K, D, E, J, F, G, and H), nine of which are essential. The nonessential genes are E and K.[8][9] Several of the genes have overlapping reading frames.[10][11] Protein A* is encoded within protein A. It lacks ~1/3 of the amino acids from the N terminal of the A protein and is encoded in the same frame as the A protein. It is translated from an internal start site within the messenger RNA. Gene E is encoded with gene D with a +1 frameshift. Gene K overlaps genes A, B, and C. The origin of replication lies within a 30 base sequence.[12] The entire 30 base sequence is required for replication.[13]

Molecular biology

The major capsid protein (F) has 426 amino acids, the major spike protein (G) has 175 amino acids, the small DNA-binding protein (J) has 25–40 amino acids, and the DNA pilot protein (H) has 328 amino acids.[14] The major folding motif of protein F is the eight-stranded antiparallel beta barrel common to many viral capsid proteins.[15] The G protein is a tight beta barrel with its strands running radially outward. The G proteins occur in groups of five forming 12 spikes that enclose a hydrophilic channel. The highly basic J protein lacks any secondary structure and is situated in an interior cleft of the F protein. It has no acidic amino acid residues in the protein and the twelve basic residues are concentrated in two clusters in the N-terminus separated by a proline-rich region.

Assembly of the virion uses two scaffolding proteins, internal scaffolding protein B and external scaffolding protein D. The function of protein B seems to be to lower the amount of protein D needed by the virion for assembly.[16] Protein H is a multifunctional structural protein required for piloting the viral DNA into the host cell interior during the entry process. Protein E is a 91-amino acid membrane protein that causes host cell lysis by inhibiting the host translocase MraY.[17] This inhibitory activity is located within the N terminal 29 amino acids.[18] Protein A is a single strand endonuclease[19] and is responsible for the initiation of viral DNA replication.[20] It catalyses cleavage and ligation of a phosphodiester bond between a G and A nucleotide residue pair at the phi X origin.[21] It may not be essential for phage viability but burst sizes are reduced by 50% when it is mutated.[22] Protein A* inhibits host DNA replication.[23] Unlike protein A it is capable of cleaving the phi X viral DNA in the presence of single-stranded binding protein of the host.[24] Protein A*, like Protein A, may not be required for phage viability.[25] Protein C increases the fidelity of the termination and reinitiation reactions and is required for the packagaging of the viral DNA in to the protein shell.[26] Protein K has 56 amino acids and is found in the membrane of the host cell. It appears to be able to increase the burst size of the virus.[27]

Taxonomy

This family is divided into two subfamilies: Gokushovirinae and Bullavirinae (former genus Microvirus). These groups differ in their hosts, genome structure, and viron composition. The name Gokushovirinae is derived from the Japanese for very small. Gokushoviruses are currently known to infect only obligate intra-cellular parasites. The members of the subfamily Bullavirinae all infect Enterobacteria.

A putative third grouping has been proposed—Alpavirinae—which infect the order Bacteroidales.[7] This a group of viruses known only as prophages and additional work on these viruses seems indicated before subfamily status is granted.

A fourth clade has been proposed—Pichovirinae.[28] This clade has a genome organisation that differs from the other members of this family. The name is derived from picho which means small in Occitan.

Another virus has been isolate from the turkey gut with features similar to other microviruses but quite distinct from the known species.[29]

Notes

Members of the subfamily Bullavirinae (former genus Microvirus) have four structural proteins: major capsid protein F, major spike protein G, a small DNA-binding protein J (25 - 40 amino acids in length) and DNA pilot protein H. Assembly of the viron uses two scaffolding proteins, internal scaffolding protein B and external scaffolding protein D. Protein H is a multifunctional structural protein required for piloting the viral DNA into the host cell interior during the entry process. The genomes are between 5.3 and 6.2 kilobases (kb) in length.

Members of this subfamily can be separated into three main clades according to genome sizes.[30] Size variability within the groups occurs mainly as a result of insertions and deletions of the intergenic regions. Viruses are assigned according to their similarity to known lab based strains—the ΦX174-like clade, G4-like clade and the α3-like clade. The ΦX174-like clade of microviridae have the smallest and least variable genomes (5,386–5,387 bp); the G4-like clade varies in size from 5,486–5,487 bp; while the largest genome sized group is the α3-like clade with genomes ranging from 6,061–6259bp.

Members of the subfamily Gokushovirinae have only two structural proteins: capsid proteins F (Virus Protein 1) and DNA pilot protein H (Virus Protein 2) and do not use scaffolding proteins. They also possess 'mushroom-like' protrusions positioned at the three-fold axes of symmetry of their icosahedral capsids. These are formed by large insertion loops within the protein F of gokushoviruses and are absent in the microviruses. They lack both the external scaffolding protein D and the major spike protein G of the species in the genus Microvirus. The genomes of this group tend to be smaller—about 4.5 kb in length. This subfamily includes the genera Bdellomicrovirus, Chlamydiamicrovirus and Spiromicrovirus.

Life cycle

There are a number of steps in the life cycle

1. Adsorption to the host via specific receptor(s)

2. Movement of the viral DNA into the host cell

3. Conversion of the single strand form to a double-stranded intermediate

This is known as the replicative form I.

4. Transcription of early genes

5. Replication of the viral genome

Viral protein A cleaves replicative form I DNA strand at the origin of replication (ori) and covalently attaches itself to the DNA, generating replicative form II molecule. Replication of the genome now begins via a rolling circle mechanism. The host's DNA polymerase converts the single-stranded DNA into double-stranded DNA.

6. Late genes are now transcribed by the host's RNA polymerase.

7. Synthesis of the new virons

Viral protein C binds to replication complex, inducing packaging of new viral positive-stranded DNA into procapsids.[31] The preinitiation complex consists of the host cell protein rep and viral A and C proteins.[32] These associate with the procapsid forming a 50S complex.

8. Maturation of the virons in the host cytoplasm

9. Release from the host

Cell lysis is mediated by the phiX174-encoded protein E, which inhibits the peptidoglycan synthesis leading to an eventual bursting of the infected cell.

References

1. Bailly, Anatole (1 January 1981). Abrégé du dictionnaire grec français. Paris: Hachette. ISBN 2010035283. OCLC 461974285.
2. Bailly, Anatole. "Greek-french dictionary online". www.tabularium.be. Retrieved 4 November 2018.
3. "Viral Zone". ExPASy. Retrieved 15 June 2015.
4. "Virus Taxonomy: 2019 Release". talk.ictvonline.org. International Committee on Taxonomy of Viruses. Retrieved 29 April 2020.
5. Keegstra W, Baas PD, Jansz HS (1979) Bacteriophage phi X174 RF DNA replication in vivo. A study by electron microscopy" J Mol Biol 135(1) 69–89
6. Fluit AC, Baas PD, Jansz HS (1986) Termination and reinitiation signals of bacteriophage phi X174 rolling circle DNA replication" Virology 154(2) 357–368
7. Krupovic M, Forterre P (2011). "Microviridae goes temperate: microvirus-related proviruses reside in the genomes of Bacteroidetes". PLOS ONE. 6 (5): e19893. doi:10.1371/journal.pone.0019893. PMC 3091885. PMID 21572966.
8. Tessman ES, Tessman I, Pollock TJ (1980) Gene K of bacteriophage phi X 174 codes for a nonessential protein" J Virol 33(1) 557-560
9. Bläsi U, Young R, Lubitz W (1988) Evaluation of the interaction of phi X174 gene products E and K in E-mediated lysis of Escherichia coli" J Virol 62(11) 4362–4364
10. Sander C, Schulz GE (1979) Degeneracy of the information contained in amino acid sequences: evidence from overlaid genes" J Mol Evol 13(3) 245–252
11. Fiddes JC, Godson GN (1979) Evolution of the three overlapping gene systems in G4 and phi X174" J Mol Biol 133(1) 19–43
12. Baas PD (1987) Mutational analysis of the bacteriophage phi X174 replication origin" J Mol Biol 198(1) 51–61
13. Fluit AC, Baas PD, Jansz HS (1985) The complete 30-base-pair origin region of bacteriophage phi X174 in a plasmid is both required and sufficient for in vivo rolling-circle DNA replication and packaging" Eur J Biochem 149(3) 579–584
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16. Chen M, Uchiyama A, Fane BA (2007) Eliminating the requirement of an essential gene product in an already very small virus: scaffolding protein B-free øX174, B-free" J Mol Biol 373(2) 308–314
17. Zheng Y, Struck DK, Young R (2009) Purification and functional characterization of phiX174 lysis protein E" Biochemistry 48(22) 4999–5006
18. Buckley KJ, Hayashi M (1986) Lytic activity localized to membrane-spanning region of phi X174 E protein. Mol Gen Genet 204(1) 120–125
19. Eisenberg S (1980) Cleavage of phi X174 single-stranded DNA by gene A protein and formation of a tight protein-DNA complex" J Virol 35(2) 409–413
20. van Mansfeld AD, Langeveld SA, Baas PD, Jansz HS, van der Marel GA, Veeneman GH, van Boom JH (1980) Recognition sequence of bacteriophage phi X174 gene A protein--an initiator of DNA replication. Nature 288(5791) 561–566
21. van Mansfeld AD, van Teeffelen HA, Baas PD, Jansz HS (1987) Two juxtaposed tyrosyl-OH groups participate in phi X174 gene A protein catalysed cleavage and ligation of DNA" Nucleic Acids Res 14(10) 4229–4238
22. Baas PD, Liewerink H, van Teeffelen HA, van Mansfeld AD, van Boom JH, Jansz HS (1987) Alteration of the ATG start codon of the A protein of bacteriophage phi X174 into an ATT codon yields a viable phage indicating that A protein is not essential for phi X174 reproduction" FEBS Lett 218(1) 119–125
23. Eisenberg S, Ascarelli R (1981) The A* protein of phi X174 is an inhibitor of DNA replication" Nucleic Acids Res 9(8) 1991–2002
24. van Mansfeld AD, van Teeffelen HA, Fluit AC, Baas PD, Jansz HS (1986) Effect of SSB protein on cleavage of single-stranded DNA by phi X gene A protein and A* protein" Nucleic Acids Res 14(4) 1845–1861
25. Colasanti J, Denhardt DT (1987) Mechanism of replication of bacteriophage phi X174. XXII. Site-specific mutagenesis of the A* gene reveals that A* protein is not essential for phi X174 DNA replication" J Mol Biol 197(1) 47–54
26. Goetz GS, Englard S, Schmidt-Glenewinkel T, Aoyama A, Hayashi M, Hurwitz J (1988) Effect of phi X C protein on leading strand DNA synthesis in the phi X174 replication pathway" J Biol Chem 263(31) 16452–16460
27. Gillam S, Atkinson T, Markham A, Smith M (1985) Gene K of bacteriophage phi X174 codes for a protein that affects the burst size of phage production" J Virol 53(2) 708–709
28. Roux S, Krupovic M, Poulet A, Debroas D, Enault F (2012). "Evolution and diversity of the Microviridae viral family through a collection of 81 new complete genomes assembled from virome reads". PLOS ONE. 7 (7): e40418. doi:10.1371/journal.pone.0040418. PMC 3394797. PMID 22808158.
29. Zsak L, Day JM, Oakley BB, Seal BS (2011) The complete genome sequence and genetic analysis of ΦCA82 a novel uncultured microphage from the turkey gastrointestinal system" Virol J 8:331.
30. Kodaira K, Nakano K, Okada S, Taketo A (1992) Nucleotide sequence of the genome of the bacteriophage alpha 3: interrelationship of the genome structure and the gene products with those of the phages, phi X174, G4 and phi K" Biochim Biophys Acta 1130(3) 277–288
31. Aoyama A, Hayashi M (1986) Synthesis of bacteriophage phi X174 in vitro: mechanism of switch from DNA replication to DNA packaging" Cell 47(1) 99–106
32. Hafenstein S and Fane BA (2002) X174 Genome-capsid interactions influence the biophysical properties of the virion: Evidence for a scaffolding-like function for the genome during the final stages of morphogenesis" J Virol 76(11) 5350–5356 doi:10.1128/JVI.76.11.5350-5356.2002

Further reading

Roykta, D.R. et al., 2006. Horizontal Gene Transfer and the Evolution of Microvirid Coliphage Genomes. Journal of Bacteriology, 118(3) p1134–1142

External links

• Viralzone: Microviridae
• List of sequenced genomes
• ICTV