Corticoviridae


Corticoviridae

Chapter Contents

Corticoviridae: The Family

Corticoviridae: Member Taxa

Corticoviridae: Supporting Information

  • Authors - Corresponding author: Hanna M. Oksanen (hanna.oksanen@helsinki.fi)
  • Resources - Sequence alignments and tree files
  • Further Reading - Reviews and additional information
  • References - Literature cited

Citation

A summary of this ICTV online (10th) report chapter has been published as an ICTV Virus Taxonomy Profile article in the Journal of General Virology, and should be cited when referencing this online chapter as follows: Oksanen, H.M., and ICTV Report Consortium. 2017, ICTV Virus Taxonomy Profile: Corticoviridae, Journal of General Virology, 98, 888-889.

Summary

The Corticoviridae is a family of icosahedral, internal membrane-containing viruses with double-stranded circular DNA genomes of approximately 10 kb. Only one species, Pseudoalteromonas virus PM2, has been recognized. Pseudoalteromonas virus PM2 infects gram-negative bacteria and was isolated from seawater in 1968. Currently, PM2 does not share significant sequence similarity to any other virus. It is the first bacterial virus in which the presence of lipids in the virion has been demonstrated. Viral lipids are acquired selectively during virion assembly from the host cytoplasmic membrane. The outer protein capsid is an icosahedron with a pseudo T=21 symmetry. Since only the genus Corticovirus is recognized, the family description corresponds to the genus description.

Table 1.Corticoviridae. Characteristics of the family Corticoviridae.

Characteristic

Description

Typical member

Pseudoalteromonas virus PM2 (AF155037), species Pseudoalteromonas virus PM2, genus Corticovirus

Virion

Icosahedral, internal membrane-containing virions of about 57 nm with a single capsid protein P2, single spike protein P1 and 8 membrane-associated proteins P3-P10

Genome

10.1 kb of highly supercoiled, circular, double-stranded DNA

Replication

Rolling circle replication initiated by virus-encoded protein P12

Translation

Prokaryotic translation using viral mRNA and host ribosomes

Host Range

Bacteria, gram-negative Pseudoalteromonas strains

Taxonomy

One genus containing one species

Distinguishing features

Pseudoalteromonas virus PM2 is a virulent virus infecting gram-negative Pseudoalteromonas species (Espejo and Canelo 1968, Kivelä et al., 1999). The characteristic feature of this corticovirus is the highly supercoiled, circular, double-stranded DNA genome. The virions are composed of an icosahedral protein capsid and an internal protein-rich membrane enclosing the genome (Abrescia et al., 2008). Pseudoalteromonas virus PM2 does not share significant sequence similarity to any other virus.

Virion

Morphology

Icosahedral virions consist of an internal membrane and an outer protein capsid that has a diameter of 57 nm between facets (Figure 1.Corticoviridae) (Abrescia et al., 2008). The genome is enclosed by the membrane. The capsid consists of 200 major capsid protein P2 trimers that are organized on a pseudo T=21 lattice (Abrescia et al., 2008). Protein P2 is composed of two beta-barrels disposed normal to the capsid surface. The P2 trimers have pseudo-six-fold symmetry and the structure is stabilized by calcium ions. Spikes protrude about 8 nm from the capsid surface at the five-fold vertices. The spikes are homopentamers and formed of protein P1. P1 is composed of three beta-barrel domains arranged end to end. The distal C-terminal domains of P1 are used for receptor recognition. The N-termini of P1 form pentagonal assemblies at the vertices. The inner membrane (47 nm in diameter) contains host plasma membrane-derived phospholipids and virus-encoded proteins P3 to P10 (Kivelä et al., 2002). Transmembrane proteins P3 and P6 are organized into a lattice on the membrane vesicle surface, on which the outer protein capsid is assembled (Abrescia et al., 2008).

Figure 1.Corticoviridae. (A) Electron micrograph of negatively stained Pseudoalteromonas virus PM2 particles. The bar represents 50 nm. (B) An atomic model based upon X-ray crystallographic analysis of a virion of Pseudoalteromonas virus PM2 at 7 Å resolution, viewed along the two-fold axis of symmetry (courtesy of N.G.A. Abrescia) and (C) a schematic presentation of the virion. Capsid diameter is approximately 57 nm (from facet to facet).

Physicochemical and physical properties

The mass of the virion is about 4.5×107 Da and is distributed among protein (72%), lipid (14%) and nucleic acid (14%) (Camerini-Otero and Franklin 1975, Camerini-Otero et al., 1974). The buoyant density in CsCl is 1.28 g cm−3 and in sucrose 1.26 g cm−3, and the S20,w is 293 S (Kivelä et al., 1999, Camerini-Otero and Franklin 1975). Virions are stable at pH 6–8, and are very sensitive to ether, chloroform and detergents (Espejo and Canelo 1968). The virion stability is strongly dependent on sodium and calcium ions (Kivelä et al., 2002). Virions are sensitive to freezing.

Nucleic acid

The genome is a highly supercoiled, circular double-stranded DNA of 10,079 bp (6.6×106 Da). DNA comprises approximately 14% of the virion weight and the G+C content is 42.2%. The Pseudoalteromonas virus PM2 genome has been sequenced (Männistö et al., 1999) (AF155037).

Proteins

The genome has 21 putative genes, 10 of which have been shown to code for structural proteins (P1-P10), 7 of which encode non-structural proteins (P12-P18) and four of which are of unknown function. Proteins form about 72% of the virus particle weight.

Table 2.Corticoviridae. Pseudoalteromonas virus PM2 proteins.

Proteina

Mass (kDa)

Location/functionb

P1

37.5

Spike protein, receptor binding (S)

P2

30.2

Major capsid protein (S)

P3

10.8

Major membrane protein (S)

P4

4.4

Membrane (S)

P5

17.9

Membrane (S)

P6

14.3

Major membrane protein (S)

P7

3.6

Membrane (S)

P8

7.3

Membrane (S)

P9

24.7

Putative packaging ATPase (S)

P10

29.0

Membrane (S)

P12

73.4

Replication initiation protein (N)

P13

7.2

Transcription factor (N)

P14

11.0

Transcription factor (N)

P15

18.1

Regulative function (N)

P16

10.3

Regulative function (N)

P17

6.0

Lysis factor (N)

P18

5.7

Lysis factor (N)

a P is for protein; Arabic numeral corresponds to the Roman numeral of the gene.
b S is for structural protein; N is for non-structural protein.

Lipids

Particles are about 14% lipid by weight (Camerini-Otero and Franklin 1975). The membrane contains 34% phosphatidyl ethanolamine and 66% phosphatidyl glycerol and trace amounts of phosphatidic acid and acyl-phosphatidyl glycerol (Braunstein and Franklin 1971, Camerini-Otero and Franklin 1972, Tsukagoshi et al., 1976). The lipids are derived from the host plasma membrane, but their composition deviates from that of the host bacterium. Lipids form an internal membrane with virus-specific membrane-associated proteins.

Genome organization and replication

To infect and replicate, Pseudoalteromonas virus PM2 delivers its genome across the cell envelope of two known marine host strains: gram-negative Pseudoalteromonas species ER72M2 and BAL-31. Virions adsorb via the distal tips of the spike proteins to uncharacterized receptors (Abrescia et al., 2008). The internal membrane mediates the translocation of the supercoiled genome across the host cell envelopes, most probably via fusion in a process that is not fully understood. Replication of the viral genome, most probably by a rolling circle mechanism, takes place in proximity to the host cytoplasmic membrane. The largest virus protein, P12, encoded by gene XII, shares significant sequence similarity with the superfamily I group of replication initiation proteins (Männistö et al., 1999). The genome is organized in three operons (Figure 2.Corticoviridae). Operons OEL and OER encode early gene products: the replication initiation protein P12 and transcription regulatory proteins P13, P14, P15 and P16. Expression of the genes for structural proteins is under the control of the late promoter (OL), which is activated by the virus-encoded transcription factors P13 and P14 (Mannistö et al., 2003). The mature virions are released from the cell by lysis. Lysis factor P17 permeabilizes the cytoplasmic membrane and acts like a holin, whereas lysis factor P18 disrupt the outer membrane, and peptidoglycan is most probably disrupted by host lytic factors (Krupovic et al., 2007).

Figure 2.Corticoviridae. Genome organization of Pseudoalteromonas virus PM2. The genome is a 10,079 bp highly supercoiled, circular double-stranded DNA molecule containing 17 genes (Roman numerals) and 4 additional ORFs (letters) the arrows indicating orientations and three operons (OER, OEL and OL). ORFs known to code for functional proteins are classified as genes and given a Roman numeral. The different colours indicate the ORFs encoding putative proteins (yellow), a gene for replication initiation protein (orange) and the following groups of genes: transcriptional regulation (magenta), structural proteins (blue) and lysis (green). Positions of the origin of replication (ORI) and the first nucleotide (marked as 1) are indicated.

Biology

Pseudoalteromonas virus PM2 is virulent and replicates in two known strains of marine host bacteria of the genus Pseudoalteromonas. Although the virus is virulent and the sole member of the family Corticoviridae, comparative genomic approaches have shown that integrated corticoviral genetic elements commonly reside within aquatic bacterial chromosomes (Krupovic and Bamford 2007)

Member Species

SpeciesVirus name(s)Exemplar isolateExemplar accession numberExemplar RefSeq numberAvailable sequenceOther isolatesOther isolate accession numbersVirus Abbreviation(s)
Pseudoalteromonas virus PM2Pseudoalteromonas virus PM2PM2AF155037NC_000867Complete genomePM2

Virus names, the choice of exemplar isolates, and virus abbreviations, are not official ICTV designations.

Derivation of names

Cortico: from Latin cortex, “crust”, “bark”.

Similarity with other taxa

The virion of corticoviruses resembles that of other tailless icosahedral viruses with an internal membrane, such as viruses in the family Tectiviridae, which have a lipid bilayer underneath the isometric protein capsid. Corticoviruses and tectiviruses appear to differ in genome organization and infection mechanism, since no tectivirus-specific, tail-like membrane tube is seen upon corticovirus infection. Pseudoalteromonas virus PM2 major capsid protein is a trimeric protein with two beta-barrels forming hexagonal capsomers (Abrescia et al., 2008). The same viral jelly-roll fold has also been described at least for Salmonella virus PRD1 (family Tectiviridae) (Benson et al., 1999), the archaeal Sulfolobus turreted icosahedral virus 1 (STIV; family Turriviridae) (Maaty et al., 2006), human adenoviruses (family Adenoviridae) (Rux et al., 2003), and large eukaryotic viruses Paramecium bursaria Chlorella virus 1 (family Phycodnaviridae) (Nandhagopal et al., 2002) and Chilo iridescent virus (family Iridoviridae), as well as Mimivirus-dependent virus Sputnik (family Lavidaviridae) (Zhang et al., 2012). In addition, bacterial and archaeal viruses in the family Sphaerolipoviridae most probably share the same major capsid fold (Gil-Carton et al., 2015, Demina et al., 2016).

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