Mimivirus

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Mimivirus
Giant Mimivirus with satellite Sputnik virophages.png
Mimivirus with two satellite Sputnik virophages (arrows) [1]
Virus classification OOjs UI icon edit-ltr.svg
(unranked): Virus
Realm: Varidnaviria
Kingdom: Bamfordvirae
Phylum: Nucleocytoviricota
Class: Megaviricetes
Order: Imitervirales
Family: Mimiviridae
Genus:Mimivirus
Species[ citation needed ]
Schematic drawing of a virion of genus Mimivirus (cross section and side view) showing filaments ("hairs") and stargate (downside) Mimivirus virion.png
Schematic drawing of a virion of genus Mimivirus (cross section and side view) showing filaments ("hairs") and stargate (downside)

Mimivirus is a genus of giant viruses, in the family Mimiviridae . Amoeba serve as their natural hosts. [2] [3] This genus contains a single identified species named Acanthamoeba polyphaga mimivirus (APMV). It also refers to a group of phylogenetically related large viruses. [4]

Contents

In colloquial speech, APMV is more commonly referred to as just "mimivirus". Mimivirus, short for "mimicking microbe", is so called to reflect its large size and apparent Gram-staining properties. [5]

Mimivirus has a large and complex genome compared with most other viruses. Until 2013, when a larger virus Pandoravirus was described, it had the largest capsid diameter of all known viruses. [6]

History

APMV was discovered accidentally in 1992 within the amoeba Acanthamoeba polyphaga , after which it is named, during research into legionellosis by researchers from Marseille and Leeds. [7] The virus was observed in a Gram stain and mistakenly thought to be a Gram-positive bacterium. As a consequence it was named Bradfordcoccus, after Bradford, England, where the amoeba had originated. In 2003, researchers at the Université de la Méditerranée in Marseille, France, published a paper in Science identifying the micro-organism as a virus. It was given the name "mimivirus" (for "mimicking microbe") as it resembles a bacterium on Gram staining. [8]

The same team that discovered the mimivirus later discovered a slightly larger virus, dubbed the mamavirus, and the Sputnik virophage that infects it. [9]

Classification

Mimivirus has been placed into a viral family by the International Committee on Taxonomy of Viruses as a member of the Mimiviridae , [10] and has been placed into Group I of the Baltimore classification system. [11]

Although not strictly a method of classification, mimivirus joins a group of large viruses known as nucleocytoplasmic large DNA viruses (NCLDV). They are all large viruses which share both molecular characteristics and large genomes. The mimivirus genome also possesses 21 genes encoding homologs to proteins which are seen to be highly conserved in the majority of NCLDVs, and further work suggests that mimivirus is an early divergent of the general NCLDV group. [8]

Structure

A: AFM image of several surface fibers attached to a common central feature. B: AFM image of two detached surface fibers of Mimivirus. C: CryoEM image of a Mimivirus after partial digestion of fibrils with Bromelain. D: AFM image of internal fibers of Mimivirus Mimivirus fibers - journal.pbio.1000092.g007.png
A: AFM image of several surface fibers attached to a common central feature. B: AFM image of two detached surface fibers of Mimivirus. C: CryoEM image of a Mimivirus after partial digestion of fibrils with Bromelain. D: AFM image of internal fibers of Mimivirus

The mimivirus is the fourth-largest virus, after the Megavirus chilensis , Pandoravirus and Pithovirus . Mimivirus has a capsid diameter of 400 nm. Protein filaments measuring 100 nm project from the surface of the capsid, bringing the total length of the virus up to 600 nm. Variation in scientific literature renders these figures as highly approximate, with the "size" of the virion being casually listed as anywhere between 400 nm and 800 nm, depending on whether total length or capsid diameter is actually quoted.[ citation needed ]

Its capsid appears hexagonal under an electron microscope, therefore the capsid symmetry is icosahedral. [12] It does not appear to possess an outer viral envelope, suggesting that the virus does not exit the host cell by exocytosis. [13] Mimivirus shares several morphological characteristics with all members of the NCLDV group of viruses. The condensed central core of the virion appears as a dark region under the electron microscope. The large genome of the virus resides within this area. An internal lipid layer surrounding the central core is present in all other NCLDV viruses, so this features may also be present in mimivirus. [12]

Several mRNA transcripts can be recovered from purified virions. Like other NCLDVs, transcripts for DNA polymerase, a capsid protein and a TFII-like transcription factor were found. However, three distinct aminoacyl tRNA synthetase enzyme transcripts and four unknown mRNA molecules specific to mimivirus were also found. These pre-packaged transcripts can be translated without viral gene expression and are likely to be necessary to Mimivirus for replication. Other DNA viruses, such as the Human cytomegalovirus and Herpes simplex virus type-1 , also feature pre-packaged mRNA transcripts. [13]

GenusStructure Symmetry CapsidGenomic arrangementGenomic segmentation
MimivirusIcosahedralT = 972–1141 or T = 1200 (h = 19 ± 1, k = 19 ± 1)LinearMonopartite

Genome

The mimivirus genome is a linear, double-stranded molecule of DNA with 1,181,404 base pairs in length. [14] This makes it one of the largest viral genomes known, outstripping the next-largest virus genome of the Cafeteria roenbergensis virus by about 450,000 base pairs. In addition, it is larger than at least 30 cellular clades. [15]

In addition to the large size of the genome, mimivirus possesses an estimated 979 protein-coding genes, far exceeding the minimum 4 genes required for viruses to exist (c.f. MS2 and Qβ viruses). [16] Analysis of its genome revealed the presence of genes not seen in any other viruses, including aminoacyl tRNA synthetases, and other genes previously thought only to be encoded by cellular organisms. Like other large DNA viruses, mimivirus contains several genes for sugar, lipid and amino acid metabolism, as well as some metabolic genes not found in any other virus. [13] Roughly 90% of the genome was of coding capacity, with the other 10% being "junk DNA".[ citation needed ]

Replication

CryoEM reconstruction of Mimivirus A) - C) Surface-shaded rendering of cryoEM reconstruction of untreated Mimivirus D) The starfish-associated vertex was removed to show the internal nucleocapsid E) Central slice of the reconstruction looking from the side of the particle F) Central slice of the reconstruction looking along the 5-fold axis from the starfish-shaped feature The coloring is based on radial distance from the center of the virus Gray is from 0 to 1,800 A Red from 1,800 to 2,100 A Rainbow coloring from red to blue between 2,100 and 2,500 A Cryoelectron microscopy of the Giant Mimivirus - journal.pbio.1000092.g005.png
CryoEM reconstruction of Mimivirus
A) – C) Surface-shaded rendering of cryoEM reconstruction of untreated Mimivirus
D) The starfish-associated vertex was removed to show the internal nucleocapsid
E) Central slice of the reconstruction looking from the side of the particle
F) Central slice of the reconstruction looking along the 5-fold axis from the starfish-shaped feature
The coloring is based on radial distance from the center of the virus
Gray is from 0 to 1,800 Å
Red from 1,800 to 2,100 Å
Rainbow coloring from red to blue between 2,100 and 2,500 Å

The stages of mimivirus replication are not well known, but as a minimum it is known that mimivirus attaches to a chemical receptor on the surface of an amoeba cell and is taken into the cell. Once inside, an eclipse phase begins, in which the virus disappears and all appears normal within the cell. After about 4 hours small accumulations can be seen in areas of the cell. 8 hours after infection many mimivirus virions are clearly visible within the cell. The cell cytoplasm continues to fill with newly synthesised virions, and about 24 hours after initial infection the cell likely bursts open to release the new mimivirus virions. [13]

Little is known[ citation needed ][ when? ] about the details of this replication cycle, most obviously attachment to the cell surface and entry, viral core release, DNA replication, transcription, translation, assembly and release of progeny virions. However, scientists have established the general overview given above using electron micrographs of infected cells.[ citation needed ] These micrographs show mimivirus capsid assembly in the nucleus, acquisition of an inner lipid membrane via budding from the nucleus, and particles similar to those found in many other viruses, including all NCLDV members. These particles are known in other viruses as viral factories and allow efficient viral assembly by modifying large areas of the host cell.[ citation needed ]

GenusHost detailsTissue tropismEntry detailsRelease detailsReplication siteAssembly siteTransmission
MimivirusZooplanktonNoneUnknownUnknownCytoplasmNucleusPassive diffusion

Pathogenicity

Mimivirus may be a causative agent of some forms of pneumonia; this is based mainly on indirect evidence in the form of antibodies to the virus discovered in pneumonia patients. [17] However, the classification of mimivirus as a pathogen is tenuous at present as there have been only a couple of papers published potentially linking mimivirus to actual cases of pneumonia. A significant fraction of pneumonia cases are of unknown cause, [18] though a mimivirus has been isolated from a Tunisian woman suffering from pneumonia. [19] There is evidence that mimivirus can infect macrophages. [20]

Implications for defining "life"

Mimivirus shows many characteristics which place it at the boundary between living and non-living. It is as large as several bacterial species, such as Rickettsia conorii and Tropheryma whipplei , possesses a genomic size comparable to that of several bacteria, including those above, and codes for products previously not thought to be encoded by viruses (including a kind of collagen [21] ). In addition, mimivirus has genes coding for nucleotide and amino acid synthesis, which even some small obligate intracellular bacteria lack. They do, however, lack any genes for ribosomal proteins, making mimivirus dependent on a host cell for protein translation and energy metabolism.[ citation needed ] [21]

Because its lineage is very old and could have emerged prior to cellular organisms, [22] [23] Mimivirus has added to the debate over the origins of life. Some genes that code for characteristics unique to Mimivirus, including those coding for the capsid, have been conserved in a variety of viruses which infect organisms from all domains. This has been used to suggest that Mimivirus is related to a type of DNA virus that emerged before cellular organisms and played a key role in the development of all life on Earth. [22] An alternative hypothesis is that there were three distinct types of DNA viruses that were involved in generating the three known domains of life—eukarya, archaea and bacteria. [23] It has been suggested that Mimivirus and similar kinds are remnants of a "fourth domain" of life, and that other giant virus may represent other ancient domains. [21]

Nevertheless, mimivirus does not exhibit the following characteristics, all of which are part of many conventional definitions of life:[ citation needed ]

See also

Related Research Articles

Viral evolution is a subfield of evolutionary biology and virology that is specifically concerned with the evolution of viruses. Viruses have short generation times, and many—in particular RNA viruses—have relatively high mutation rates. Although most viral mutations confer no benefit and often even prove deleterious to viruses, the rapid rate of viral mutation combined with natural selection allows viruses to quickly adapt to changes in their host environment. In addition, because viruses typically produce many copies in an infected host, mutated genes can be passed on to many offspring quickly. Although the chance of mutations and evolution can change depending on the type of virus, viruses overall have high chances for mutations.

<span class="mw-page-title-main">Viral replication</span> Formation of biological viruses during the infection process

Viral replication is the formation of biological viruses during the infection process in the target host cells. Viruses must first get into the cell before viral replication can occur. Through the generation of abundant copies of its genome and packaging these copies, the virus continues infecting new hosts. Replication between viruses is greatly varied and depends on the type of genes involved in them. Most DNA viruses assemble in the nucleus while most RNA viruses develop solely in cytoplasm.

<span class="mw-page-title-main">Viroplasm</span>

A viroplasm, sometimes called "virus factory" or "virus inclusion", is an inclusion body in a cell where viral replication and assembly occurs. They may be thought of as viral factories in the cell. There are many viroplasms in one infected cell, where they appear dense to electron microscopy. Very little is understood about the mechanism of viroplasm formation.

<span class="mw-page-title-main">Virophage</span> Viral parasites of giant viruses

Virophages are small, double-stranded DNA viral phages that require the co-infection of another virus. The co-infecting viruses are typically giant viruses. Virophages rely on the viral replication factory of the co-infecting giant virus for their own replication. One of the characteristics of virophages is that they have a parasitic relationship with the co-infecting virus. Their dependence upon the giant virus for replication often results in the deactivation of the giant viruses. The virophage may improve the recovery and survival of the host organism.

<span class="mw-page-title-main">Virus</span> Infectious agent that replicates in cells

A virus is a submicroscopic infectious agent that replicates only inside the living cells of an organism. Viruses infect all life forms, from animals and plants to microorganisms, including bacteria and archaea. Viruses are found in almost every ecosystem on Earth and are the most numerous type of biological entity. Since Dmitri Ivanovsky's 1892 article describing a non-bacterial pathogen infecting tobacco plants and the discovery of the tobacco mosaic virus by Martinus Beijerinck in 1898, more than 11,000 of the millions of virus species have been described in detail. The study of viruses is known as virology, a subspeciality of microbiology.

<span class="mw-page-title-main">Sputnik virophage</span> Subviral agent

Mimivirus-dependent virus Sputnik is a subviral agent that reproduces in amoeba cells that are already infected by a certain helper virus; Sputnik uses the helper virus's machinery for reproduction and inhibits replication of the helper virus. It is known as a virophage, in analogy to the term bacteriophage.

<i>Mimiviridae</i> Family of viruses

Mimiviridae is a family of viruses. Amoeba and other protists serve as natural hosts. The family is divided in up to 4 subfamilies. Viruses in this family belong to the nucleocytoplasmic large DNA virus clade (NCLDV), also referred to as giant viruses.

Mamavirus is a large and complex virus in the Group I family Mimiviridae. The virus is exceptionally large, and larger than many bacteria. Mamavirus and other mimiviridae belong to nucleocytoplasmic large DNA virus (NCLDVs) family. Mamavirus can be compared to the similar complex virus mimivirus; mamavirus was so named because it is similar to but larger than mimivirus.

<i>Cafeteria roenbergensis virus</i> Species of virus

Cafeteria roenbergensis virus (CroV) is a giant virus that infects the marine bicosoecid flagellate Cafeteria roenbergensis, a member of the microzooplankton community.

A giant virus, sometimes referred to as a girus, is a very large virus, some of which are larger than typical bacteria. All known giant viruses belong to the phylum Nucleocytoviricota.

<i>Megavirus</i> Genus of viruses

Megavirus is a viral genus, phylogenetically related to Acanthamoeba polyphaga mimivirus (APMV). In colloquial speech, Megavirus chilense is more commonly referred to as just "Megavirus". Until the discovery of pandoraviruses in 2013, it had the largest capsid diameter of all known viruses, as well as the largest and most complex genome among all known viruses.

<i>Pandoravirus</i> Genus of giant virus possessing a large double-stranded DNA genome

Pandoravirus is a proposed genus of giant virus, first discovered in 2013. It is the third largest in physical size of any known viral genus, behind Pithovirus and Megaklothovirus. Pandoraviruses have double stranded DNA genomes, with the largest genome size of any known viral genus.

<i>Alphapithovirus</i> Genus of viruses

Alphapithovirus, is a genus of giant virus known from two species, Alphapithovirus sibericum, which infects amoebas, and Alphapithovirus massiliense. It is DNA-based and is a member of the nucleocytoplasmic large DNA viruses clade. It was discovered in 2014, when a viable specimen was found in a 30,000-year-old ice core harvested from permafrost in Siberia, Russia.

<span class="mw-page-title-main">Zamilon virophage</span> Virus type

Mimivirus-dependent virus Zamilon, or Zamilon, is a virophage, a group of small DNA viruses that infect protists and require a helper virus to replicate; they are a type of satellite virus. Discovered in 2013 in Tunisia, infecting Acanthamoeba polyphaga amoebae, Zamilon most closely resembles Sputnik, the first virophage to be discovered. The name is Arabic for "the neighbour". Its spherical particle is 50–60 nm in diameter, and contains a circular double-stranded DNA genome of around 17 kb, which is predicted to encode 20 polypeptides. A related strain, Zamilon 2, has been identified in North America.

<i>Faustovirus</i> Genus of viruses

Faustovirus is a genus of giant virus which infects amoebae associated with humans. The virus was first isolated in 2015 and shown to be around 0.2 micrometers in diameter with a double stranded DNA genome of 466 kilobases predicted to encode 451 proteins. Although classified as a nucleocytoplasmic large DNA virus (NCLDV), faustoviruses share less than a quarter of their genes with other NCLDVs; however, ~46% are homologous to bacterial genes and the remainder are orphan genes (ORFans). Specifically, the gene encoding the major capsid protein (MCP) of faustovirus is different than that of its most closely related giant virus, asfivirus, as well as other NCLDVs. In asfivirus, the gene encoding MCP is a single genomic fragment of ~2000 base pairs (bp), however, in faustovirus the MCP is encoded by 13 exons separated by 12 large introns. The exons have a mean length of 149 bp and the introns have a mean length of 1,273 bp. The presence of introns in faustovirus genes is highly unusual for viruses.

<i>Tupanvirus</i> Proposed genus of viruses

Tupanvirus is a genus of viruses first described in 2018. The genus is composed of two species of virus that are in the giant virus group. Researchers discovered the first isolate in 2012 from deep water sediment samples taken at 3,000 m depth off the coast of Brazil. The second isolate was collected from a soda lake in Southern Nhecolândia, Brazil in 2014. They are named after Tupã (Tupan), a Guaraní thunder god, and the places they were found. These are the first viruses reported to possess genes for amino-acyl tRNA synthetases for all 20 standard amino acids.

<span class="mw-page-title-main">Chrysochromulina ericina virus</span> Giant virus

Chrysochromulina ericina virus 01B, or simply Chrysochromulina ericina virus (CeV) is a giant virus in the family Mimiviridae infecting Haptolina ericina, a marine microalgae member of the Haptophyta. CeV is a dsDNA virus.

<i>Varidnaviria</i> Realm of viruses

Varidnaviria is a realm of viruses that includes all DNA viruses that encode major capsid proteins that contain a vertical jelly roll fold. The major capsid proteins (MCP) form into pseudohexameric subunits of the viral capsid, which stores the viral deoxyribonucleic acid (DNA), and are perpendicular, or vertical, to the surface of the capsid. Apart from this, viruses in the realm also share many other characteristics, such as minor capsid proteins (mCP) with the vertical jelly roll fold, an ATPase that packages viral DNA into the capsid, and a DNA polymerase that replicates the viral genome.

Nucleocytoviricota is a phylum of viruses. Members of the phylum are also known as the nucleocytoplasmic large DNA viruses (NCLDV), which serves as the basis of the name of the phylum with the suffix -viricota for virus phylum. These viruses are referred to as nucleocytoplasmic because they are often able to replicate in both the host's cell nucleus and cytoplasm.

Virosphere was coined to refer to all those places in which viruses are found or which are affected by viruses. However, more recently virosphere has also been used to refer to the pool of viruses that occurs in all hosts and all environments, as well as viruses associated with specific types of hosts, type of genome or ecological niche.

References

  1. ↑ Duponchel, S. and Fischer, M.G. (2019) "Viva lavidaviruses! Five features of virophages that parasitize giant DNA viruses". PLoS pathogens, 15(3). doi:10.1371/journal.ppat.1007592. CC-BY icon.svg Material was copied from this source, which is available under a Creative Commons Attribution 4.0 International License.
  2. ↑ "Viral Zone". ExPASy. Retrieved 15 June 2015.
  3. ↑ ICTV. "Virus Taxonomy: 2014 Release" . Retrieved 15 June 2015.
  4. ↑ Ghedin, E.; Claverie, J. (August 2005). "Mimivirus relatives in the Sargasso sea". Virology Journal . 2: 62. arXiv: q-bio/0504014 . Bibcode:2005q.bio.....4014G. doi: 10.1186/1743-422X-2-62 . PMC   1215527 . PMID   16105173.
  5. ↑ Wessner, D. R. (2010). "Discovery of the Giant Mimivirus". Nature Education. 3 (9): 61. Retrieved 7 January 2012.
  6. ↑ "World's biggest virus found in sea off Chile". London: Telegraph UK. 11 October 2011. Archived from the original on 11 October 2011. Retrieved 11 November 2011.
  7. ↑ Richard Birtles; TJ Rowbotham; C Storey; TJ Marrie; Didier Raoult (29 March 1997). "Chlamydia-like obligate parasite of free-living amoebae". The Lancet. 349 (9056): 925–926. doi:10.1016/S0140-6736(05)62701-8. PMID   9093261. S2CID   5382736.
  8. 1 2 Bernard La Scola; Stéphane Audic; Catherine Robert; Liang Jungang; Xavier de Lamballerie; Michel Drancourt; Richard Birtles; Jean-Michel Claverie; Didier Raoult. (2003). "A giant virus in amoebae". Science. 299 (5615): 2033. doi:10.1126/science.1081867. PMID   12663918. S2CID   39606235.
  9. ↑ Pearson H (2008). "'Virophage' suggests viruses are alive". Nature. 454 (7205): 677. Bibcode:2008Natur.454..677P. doi:10.1038/454677a. ISSN   0028-0836. PMID   18685665.
  10. ↑ Claverie J-M (2010). Mahy W.J. and Van Regenmortel M. H. V. (ed.). Desk Encyclopedia of General Virology (1 ed.). Oxford: Academic Press. p. 189.
  11. ↑ Leppard, Keith; Nigel Dimmock; Easton, Andrew (2007). Introduction to Modern Virology (6 ed.). Blackwell Publishing Limited. pp.  469–470. ISBN   9781405136457.
  12. 1 2 Xiao C, Kuznetsov YG, Sun S, Hafenstein SL, Kostyuchenko VA, Chipman PR, Suzan-Monti M, Raoult D, McPherson A, Rossmann MG (April 2009). "Structural studies of the giant mimivirus". PLOS Biology. 7 (4): e92. doi: 10.1371/journal.pbio.1000092 . PMC   2671561 . PMID   19402750.
  13. 1 2 3 4 Suzan-Monti M, La Scola B, Raoult D (April 2006). "Genomic and evolutionary aspects of Mimivirus". Virus Research. 117 (1): 145–55. doi:10.1016/j.virusres.2005.07.011. PMID   16181700.
  14. ↑ "Acanthamoeba polyphaga mimivirus, complete genome". NCBI.
  15. ↑ Claverie, Jean-Michel; et al. (2006). "Mimivirus and the emerging concept of 'giant' virus". Virus Research. 117 (1): 133–144. arXiv: q-bio/0506007 . doi:10.1016/j.virusres.2006.01.008. PMID   16469402. S2CID   8791457.
  16. ↑ Prescott, Lansing M. (1993). Microbiology (2nd ed.). Dubuque, IA: Wm. C. Brown Publishers. ISBN   0-697-01372-3.[ page needed ]
  17. ↑ La Scola B, Marrie T, Auffray J, Raoult D (2005). "Mimivirus in pneumonia patients". Emerg Infect Dis. 11 (3): 449–52. doi:10.3201/eid1103.040538. PMC   3298252 . PMID   15757563. Archived from the original on 24 April 2009. Retrieved 10 September 2017.
  18. ↑ Marrie TJ, Durant H, Yates L (1989). "Community-Acquired Pneumonia Requiring Hospitalization: 5-Year Prospective Study". Reviews of Infectious Diseases. 11 (4): 586–99. doi:10.1093/clinids/11.4.586. PMID   2772465.
  19. ↑ Saadi H, Pagnier I, Colson P, Cherif JK, Beji M, Boughalmi M, Azza S, Armstrong N, Robert C, Fournous G, La Scola B, Raoult D (August 2013). "First isolation of Mimivirus in a patient with pneumonia". Clinical Infectious Diseases. 57 (4): e127–34. doi: 10.1093/cid/cit354 . PMID   23709652.
  20. ↑ Ghigo, Eric; Kartenbeck, Jürgen; Lien, Pham; Pelkmans, Lucas; Capo, Christian; Mege, Jean-Louis; Raoult, Didier (13 June 2008). "Ameobal Pathogen Mimivirus Infects Macrophages through Phagocytosis". PLOS Pathogens. 4 (6): e1000087. doi: 10.1371/journal.ppat.1000087 . PMC   2398789 . PMID   18551172.
  21. 1 2 3 Garry Hamilton (23 January 2016). "How giant viruses could rewrite the story of life on Earth". New Scientist .
  22. 1 2 Siebert, Charles (15 March 2006). "Unintelligent Design". Discover Magazine.
  23. 1 2 Forterre, Patrick (2006). "Three RNA cells for ribosomal lineages and three DNA viruses to replicate their genomes: A hypothesis for the origin of cellular domain". PNAS . 103 (10): 3669–3674. Bibcode:2006PNAS..103.3669F. doi: 10.1073/pnas.0510333103 . PMC   1450140 . PMID   16505372.

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