Microviridae: Microviruses and Gokushoviruses

Abstract

Members of the Microviridae comprise two subfamilies. The microviruses (Greek for small), which infect free‐living bacteria, are among the fastest known replicating viruses. Gokushoviruses (Japanese for very small) occupy a unique niche, infecting obligate intracellular bacteria, such as Chlamydia and Bdellovibrio, or mollicutes, bacteria without a cell wall. All members of the family contain small (4000–6000 bases), circular, single‐stranded deoxyribonucleic acid (ssDNA) genomes of positive polarity, which are packaged inside small (∼25 nm diameter) T=1 icosahedral capsids. The other icosahedral, ssDNA virus families: Parvoviridae, Circoviridae, Nanoviridae and Geminiviridae; share most of these properties, suggesting a large super family spanning several domains of life. The most well known member of the Microviridae, ϕX174, has been extensively used to study the fundamental mechanisms of DNA replication and capsid assembly. The latter is uniquely dependent on two scaffolding proteins, and has become a model system for experimental evolution.

Key Concepts:

  • Whilst overlapping reading frames increase the amount of genetic information encoded in small genomes, they do not appear to significantly impact the ability of the virus to genetically adapt to selective pressures.

  • Due to the genome's positive polarity, DNA replication must commence before viral genes can be transcribed.

  • Microvirus DNA replication occurs in three distinct stages: (1) ssDNA is first converted to a double‐stranded molecule, (2) amplification of the double‐stranded molecule, (3) single‐stranded genomic DNA synthesis and packaging.

  • Genomic DNA synthesis and packaging are concurrent processes; thus, a genome is not synthesised unless there exists a capsid in which to package it.

  • Gene expression is controlled by the finely tuned interplay of cis‐acting genetic elements: promoters, ribosome binding sites, mRNA stability sequences and transcription terminators.

  • Microviruses are distinguished by their two scaffolding protein system, whereas Gokushoviruses utilise a single scaffolding protein.

  • Capsid assembly is mediated by scaffolding proteins, which induce conformational switches in the viral coat protein to control the timing and fidelity of morphogenesis.

  • Cell lysis is achieved by inhibiting host cell wall biosynthesis, a mechanism reminiscent of some antibiotics.

Keywords: bacteriophage; icosahedral; ssDNA; atomic structure; scaffolding protein; procapsid

Figure 1.

Virion and procapsids structures. (a) Atomic structure of ϕX174, a microvirus. (b) CryoEM image reconstruction of SpV4, a gokushovirus. (c) CryoEM image reconstruction of the ϕX174 procapsid. The external scaffolding protein is shaded in light green, the major spike protein in blue, and the viral coat protein in magenta. The triangle highlights an asymmetric unit, which contains one coat, one major spike and four external scaffolding proteins. The oval, pentagon and triangle depict the respective two‐, five‐, and three‐fold axes of symmetry. (d) The atomic structure of the four D proteins found in the asymmetric unit. Subunits D1, D2, D3 and D4 are depicted in green, yellow, red and turquoise, respectively.

Figure 2.

Genetic maps. (a) Linear depictions of microvirus and gokushovirus genetic maps. With the exception of the HA intercistronic inset, maps are drawn to scale. For SpV4, the genes corresponding to the ϕMH2K and Chp2 genes are given in parentheses. (b) Circular depiction of the Microvirus genetic map. (c) Transcription map of ϕX174. Promoters and terminators are depicted with ‘P's’ and ‘T's,’ respectively. The subscript letter demarks the location and name of the promoter or terminator. Grey lines represent transcripts. The width of the line reflects the gene transcript's relative abundance in an infected cell.

Figure 3.

The ϕX174 lifecycle. The roles and functions of the viral proteins are listed in Table . The host cell rep protein is required for proper DNA packaging.

close

References

Aoyama A and Hayashi M (1985) Effects of genome size on bacteriophage phi X174 DNA packaging in vitro. Journal of Biological Chemistry 260: 11033–11038.

Azuma J, Morita J and Komano T (1980) Process of attachment of phi X174 parental DNA to the host cell membrane. Journal of Biochemistry 88: 525–532.

Bayer ME and Starkey TW (1972) The adsorption of bacteriophage phi X174 and its interaction with Escherichia coli; a kinetic and morphological study. Virology 49: 236–256.

Bernal RA, Hafenstein S, Esmeralda R et al. (2004) The phiX174 protein J mediates DNA packaging and viral attachment to host cells. Journal of Molecular Biology 337: 1109–1122.

Bernal RA, Hafenstein S, Olson NH et al. (2003) Structural studies of bacteriophage alpha3 assembly. Journal of Molecular Biology 325: 11–24.

Bernhardt TG, Roof WD and Young R (2000) Genetic evidence that the bacteriophage phi X174 lysis protein inhibits cell wall synthesis. Proceedings of the National Academy of Science USA 97: 4297–4302.

Bernhardt TG, Struck DK and Young R (2001) The lysis protein E of phi X174 is a specific inhibitor of the MraY‐catalyzed step in peptidoglycan synthesis. Journal of Biological Chemistry 276: 6093–6097.

Blasi U, Nam K, Lubitz W et al. (1990) Translational efficiency of phi X174 lysis gene E is unaffected by upstream translation of the overlapping gene D reading frame. J Bacteriology 172: 5617–5623.

Brentlinger KL, Hafenstein S, Novak CR et al. (2002) Microviridae, a family divided: isolation, characterization, and genome sequence of phiMH2K, a bacteriophage of the obligate intracellular parasitic bacterium Bdellovibrio bacteriovorus. J Bacteriology 184: 1089–1094.

Bull J and Wichman H (1998) A revolution in evolution. Science 281: 1959.

Burch AD and Fane BA (2000a) Foreign and chimeric external scaffolding proteins as inhibitors of Microviridae morphogenesis. Journal of Virology 74: 9347–9352.

Burch AD and Fane BA (2000b) Efficient complementation by chimeric Microviridae internal scaffolding proteins is a function of the COOH‐terminus of the encoded protein. Virology 270: 286–290.

Burch AD and Fane BA (2003) Genetic analyses of putative conformation switching and cross‐species inhibitory domains in Microviridae external scaffolding proteins. Virology 310: 64–71.

Burch AD, Ta J and Fane BA (1999) Cross‐functional analysis of the Microviridae internal scaffolding protein. Journal of Molecular Biology 286: 95–104.

Chen M, Uchiyama A and Fane BA (2007) Eliminating the requirement of an essential gene product in an already very small virus: scaffolding protein B‐free oX174, B‐free. Journal of Molecular Biology 373: 308–314.

Cherwa JE Jr, Sanchez‐Soria P, Wichman HA et al. (2009) Viral adaptation to an antiviral protein enhances the fitness level to above that of the uninhibited wild type. Journal of Virology 83: 11746–11750.

Cherwa JE Jr, Uchiyama A and Fane BA (2008) Scaffolding proteins altered in the ability to perform a conformational switch confer dominant lethal assembly defects. Journal of Virology 82: 5774–5780.

Chipman PR, Agbandje‐McKenna M, Renaudin J et al. (1998) Structural analysis of the Spiroplasma virus, SpV4: implications for evolutionary variation to obtain host diversity among the Microviridae. Structure 6: 135–145.

Clarke IN, Cutcliffe LT, Everson JS et al. (2004) Chlamydiaphage Chp2, a skeleton in the phiX174 closet: scaffolding protein and procapsid identification. J Bacteriology 186: 7571–7574.

Dokland T, Bernal RA, Burch A et al. (1999) The role of scaffolding proteins in the assembly of the small, single‐stranded DNA virus phiX174. Journal of Molecular Biology 288: 595–608.

Edgell MH, Hutchison CA 3rd and Sinsheimer RL (1969) The process of infection with bacteriophage phi‐X174. 28. Removal of the spike proteins from the phage capsid. Journal of Molecular Biology 42: 547–557.

Ekechukwu MC, Oberste DJ and Fane BA (1995) Host and phi X 174 mutations affecting the morphogenesis or stabilization of the 50S complex, a single‐stranded DNA synthesizing intermediate. Genetics 140: 1167–1174.

Everson JS, Garner SA, Lambden PR et al. (2003) Host range of chlamydiaphages phiCPAR39 and Chp3. J Bacteriology 185: 6490–6492.

Fane BA and Hayashi M (1991) Second‐site suppressors of a cold‐sensitive prohead accessory protein of bacteriophage phi X174. Genetics 128: 663–671.

Feige U and Stirm S (1976) On the structure of the E. coli C cell wall lipopolysaccharide core and on its phiX174 receptor region. Biochemical and Biophysical Research Communications 71: 566–573.

Hafenstein S and Fane BA (2002) phi 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. Journal of Virology 76: 5350–5356.

Hamatake RK, Aoyama A and Hayashi M (1985) The J gene of bacteriophage phi X174: in vitro analysis of J protein function. Journal of Virology 54: 345–350.

Hayashi M, Aoyama A, Richardson DL and Hayashi NM (1988) In: Calender R and Brew JS (eds) The Bacteriophages, pp. 1–71. New York: Plenum Press.

Hayashi MN and Hayashi M (1985) Cloned DNA sequences that determine mRNA stability of bacteriophage phi X174 in vivo are functional. Nucleic Acids Research 13: 5937–5948.

Ilag LL, McKenna R, Yadav MP et al. (1994) Calcium ion‐induced structural changes in bacteriophage phi X174. Journal of Molecular Biology 244: 291–300.

Incardona NL, Tuech JK and Murti G (1985) Irreversible binding of phage phi X174 to cell‐bound lipopolysaccharide receptors and release of virus‐receptor complexes. Biochemistry 24: 6439–6446.

Jennings B and Fane BA (1997) Genetic analysis of the phi X174 DNA binding protein. Virology 227: 370–377.

Kornberg A (1980) DNA Replication. San Francisco: Freeman.

Liu BL, Everson JS, Fane B et al. (2000) Molecular characterization of a bacteriophage (Chp2) from Chlamydia psittaci. Journal of Virology 74: 3464–3469.

McKenna R, Ilag LL and Rossmann MG (1994) Analysis of the single‐stranded DNA bacteriophage phi X174, refined at a resolution of 3.0 A. Journal of Molecular Biology 237: 517–543.

Morais MC, Fisher M, Kanamaru S et al. (2004) Conformational switching by the scaffolding protein D directs the assembly of bacteriophage phiX174. Molecular Cell 15: 991–997.

Rokyta DR, Burch CL, Caudle SB et al. (2006) Horizontal gene transfer and the evolution of microvirid coliphage genomes. Journal of Bacteriology 188: 1134–1142.

Roof WD, Fang HQ, Young KD et al. (1997) Mutational analysis of slyD, an E. coli gene encoding a protein of the FKBP immunophilin family. Molecular Biology 25: 1031–1046.

Roof WD, Horne SM, Young KD et al. (1994) slyD, a host gene required for phi X174 lysis, is related to the FK506‐binding protein family of peptidyl‐prolyl cis‐trans‐isomerases. Journal of Biological Chemistry 269: 2902–2910.

Ruboyianes MV, Chen M, Dubrava MS et al. (2009) The expression of N‐terminal deletion DNA pilot proteins inhibits the early stages of phiX174 replication. Journal of Virology 83: 9952–9956.

Salim O, Skilton RJ, Lambden PR et al. (2008) Behind the chlamydial cloak: the replication cycle of chlamydiaphage Chp2, revealed. Virology 377: 440–445.

Sanger F, Coulson A, Friedmann T et al. (1978) The nucleotide sequence of bacteriophage phiX174. Journal of Molecular Biology 125: 225–246.

Siden EJ and Hayashi M (1974) Role of the gene B‐product in bacteriophage phi‐X174 development. Journal of Molecular Biology 89: 1–16.

Sinsheimer RL (1959) A single‐stranded deoxyribonucleotide acid from bacteriophage ϕX174. Journal of Molecular Biology 1: 43–53.

Sullivan W (1979) The New York Times 7 May: D13.

Tonegawa S and Hayashi M (1970) Intermediates in the assembly of phi X174. Journal of Molecular Biology 48: 219–242.

Uchiyama A, Chen M and Fane BA (2007) Characterization and function of putative substrate specificity domain in microvirus external scaffolding proteins. Journal of Virology 81: 8587–8592.

Uchiyama A, Heiman P and Fane BA (2009) N‐terminal deletions of the phiX174 external scaffolding protein affect the timing and fidelity of assembly. Virology 386: 303–309.

Yazaki K (1981) Electron microscopic studies of bacteriophage phi X174 intact and ‘eclipsing’ particles, and the genome by the staining, and shadowing method. Journal of Virology Methods 2: 159–167.

Zheng Y, Struck DK and Young R (2009) Purification and functional characterization of phiX174 lysis protein E. Biochemistry 48: 4999–5006.

Further Reading

Aoyama A, Hamatake RK and Hayashi M (1983) In vitro synthesis of bacteriophage phi X174 by purified components. Proceedings of the National Academy of Science USA 80: 4195–4199.

Dokland T, McKenna R, Ilag LL et al. (1997) Structure of a viral procapsid with molecular scaffolding. Nature 389: 308–313.

Fane BA, Brentlinger KL, Burch AD et al. (2006) ϕX174 et al. In: Calender R (ed.) The Bacteriophages, pp. 129–145. London: Oxford Press.

Fane BA and Prevelige PE Jr (2003) Mechanism of scaffolding‐assisted viral assembly. Advances in Protein Chemistry 64: 259–299.

Kornberg A (1982) Supplement to DNA Replication. San Francisco: Freeman.

Sertic V and Bulgakov N (1935) Classification et identification des typhi‐phage. Comptes Rendus des Seances de la Societe de Biologie et de ses Filiales 119: 1270–1272.

Wichman HA, Badgett MR, Scott LA et al. (1999) Different trajectories of parallel evolution during viral adaptation. Science 285: 422–424.

Wichman HA, Scott LA, Yarber CD et al. (2000) Experimental evolution recapitulates natural evolution. Philosophical Transactions of the Royal Society of London B: Biological Sciences 355: 1677–1684.

Young R and Wang I‐N (2006) Phage Lysis, The Bacteriophages, R. Calendar. 104‐128. London: Oxford.

Zlotnick A and Fane BA (2010) Mechanisms of icosahedral virus assembly. In: Agbandje‐McKenna M and McKenna R (eds) Structural Virology, pp. 180–202. London: Royal Society of Chemistry.

Contact Editor close
Submit a note to the editor about this article by filling in the form below.

* Required Field

How to Cite close
Cherwa, James E, and Fane, Bentley A(May 2011) Microviridae: Microviruses and Gokushoviruses. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0000781.pub2]