Polinton

Last updated

Polintons (also called Mavericks) are large DNA transposons which contain genes with homology to viral proteins and which are often found in eukaryotic genomes. They were first discovered in the mid-2000s and are the largest and most complex known DNA transposons. Polintons encode up to 10 individual proteins and derive their name from two key proteins, a DNA polymerase and a retroviral-like integrase. [1] [2] [3] [4] [5]

Contents

Properties

A typical polinton is around 15–20 kilobase pairs in size, though examples have been described up to 40kb. [6] Polintons encode up to 10 proteins, the key elements being the protein-primed type B DNA polymerase and the retroviral-like integrase from which they derive their name. Polintons are sometimes referred to as "self-synthesizing" transposons, because they encode the proteins necessary to replicate themselves. [5] Most polintons also encode an adenoviral-like cysteine protease, an FtsK-like ATPase, and proteins with homology to the jelly-roll fold structure of viral capsid proteins. The presence of putative capsid proteins has prompted suggestions that polintons may be able to form virions under some conditions; however, this has not been demonstrated experimentally. [3] [5] [7]

Polinton sequences contain terminal inverted repeats characteristic of transposable elements, usually on the order of 100–1000 base pairs. [3] They also possess a 6bp target site duplication sequence at the insertion site. [6]

Distribution

Polintons have been detected in all groups of eukaryotes other than the Archaeplastida (containing red algae, green algae, glaucophytes, and land plants). They are particularly common in unikonts, a group that includes animals. [3] The pathogenic parasite Trichomonas vaginalis , which causes trichomoniasis, has a unique genome composed of up to 30% polintons. [2]

Evolution

The genetic network linking various types of Bamfordvirae viruses and selfish genetic elements, represented by labeled circles. Links between circles are color-coded by the gene whose sequence homology establishes the link. Yutin 2013 bmc virophage polinton transpoviron.png
The genetic network linking various types of Bamfordvirae viruses and selfish genetic elements, represented by labeled circles. Links between circles are color-coded by the gene whose sequence homology establishes the link.

Early descriptions of polintons identified them as likely to be ancient, at least one billion years old and possibly associated with an early ancestor of modern eukaryotes. [1] Phylogenetic analyses of known polinton sequences support this ancestry model and suggest that transmission of polintons is mainly vertical [6] (though horizontal gene transfer of a polinton has been reported [9] ).

The evolutionary relationships between polintons, double-stranded DNA viruses, and selfish genetic elements are complex. The first descriptions of polintons linked them by sequence relationship to linear plasmids, bacteriophages, and adenoviruses. [1] More recently, relationships have been identified between polintons, virophages, and giant viruses. Polintons are increasingly thought to form one component of a complex genetic network linking selfish genetic elements in eukaryotic genomes with double-stranded DNA viruses. Through homology in at least one and usually several genes, polintons are evolutionarily linked to linear plasmids, virophages (especially Mavirus virophage, family Lavidaviridae ), giant viruses ( Megavirales ), Ginger 1 transposons, Tlr1 transposons, transpovirons, eukaryotic viruses of the Adenoviridae family, and bacteriophages of the Tectiviridae family. [3] [5] [8]

The Maveriviricetes class of viruses is named after their resemblance to Maverick/Polinton transposons. All the viruses mentioned are united under Bamfordvirae for their double jelly-roll capsid. [10] Some polinton-like viruses (PLVs) other than Tlr1 have also been identified, and are yet to be put into a taxon (presumably under Maveriviricetes). [3]

Discovery and nomenclature

Giant transposable elements were originally discovered in the mid-2000s, beginning with the description of a novel family of retroviral-like integrase proteins [11] which were then associated with transposable elements given the name Mavericks. [2] [12] Meanwhile, an overlapping class of transposable element was described under the name polintons, derived from the key proteins polymerase and integrase, by Vladimir Kapitonov and Jerzy Jurka. [1] Both terms continue in common use. [3] [6]

Because of their viral capsid-like proteins and self-replication abilities, it has been suggested that polintons are capable of forming virions and would properly be termed polintoviruses. [7] However, this terminology is not yet accepted and awaits experimental validation of the virion hypothesis. [3] [4]

Related Research Articles

<span class="mw-page-title-main">DNA virus</span> Virus that has DNA as its genetic material

A DNA virus is a virus that has a genome made of deoxyribonucleic acid (DNA) that is replicated by a DNA polymerase. They can be divided between those that have two strands of DNA in their genome, called double-stranded DNA (dsDNA) viruses, and those that have one strand of DNA in their genome, called single-stranded DNA (ssDNA) viruses. dsDNA viruses primarily belong to two realms: Duplodnaviria and Varidnaviria, and ssDNA viruses are almost exclusively assigned to the realm Monodnaviria, which also includes some dsDNA viruses. Additionally, many DNA viruses are unassigned to higher taxa. Reverse transcribing viruses, which have a DNA genome that is replicated through an RNA intermediate by a reverse transcriptase, are classified into the kingdom Pararnavirae in the realm Riboviria.

Metaviridae is a family of viruses which exist as Ty3-gypsy LTR retrotransposons in a eukaryotic host's genome. They are closely related to retroviruses: members of the family Metaviridae share many genomic elements with retroviruses, including length, organization, and genes themselves. This includes genes that encode reverse transcriptase, integrase, and capsid proteins. The reverse transcriptase and integrase proteins are needed for the retrotransposon activity of the virus. In some cases, virus-like particles can be formed from capsid proteins.

<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">Jerzy Jurka</span> Polish-American biologist (1950 –2014)

Jerzy Władysław Jurka was a Polish-American computational and molecular biologist. He served as the assistant director of research at the Linus Pauling Institute prior to founding the Genetic Information Research Institute. He collaborated with several notable scientists including Linus Pauling, George Irving Bell, Roy Britten, Temple Smith, and Emile Zuckerkandl. His Erdős number is 3, using the path through Temple Smith and Stanislaw Ulam.

<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.

<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.

<span class="mw-page-title-main">Mavirus</span> Genus of viruses

Mavirus is a genus of double stranded DNA virus that can infect the marine phagotrophic flagellate Cafeteria roenbergensis, but only in the presence of the giant CroV virus. The genus contains only one species, Cafeteriavirus-dependent mavirus. Mavirus can integrate into the genome of cells of C. roenbergensis, and thereby confer immunity to the population

<i>Bidensovirus</i> Genus of viruses

Bidensovirus is a genus of single stranded DNA viruses that infect invertebrates. The species in this genus were originally classified in the family Parvoviridae but were moved to a new genus because of significant differences in the genomes.

A transpoviron is a plasmid-like genetic element found in the genomes of giant DNA viruses.

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

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.

DNA transposons are DNA sequences, sometimes referred to "jumping genes", that can move and integrate to different locations within the genome. They are class II transposable elements (TEs) that move through a DNA intermediate, as opposed to class I TEs, retrotransposons, that move through an RNA intermediate. DNA transposons can move in the DNA of an organism via a single-or double-stranded DNA intermediate. DNA transposons have been found in both prokaryotic and eukaryotic organisms. They can make up a significant portion of an organism's genome, particularly in eukaryotes. In prokaryotes, TE's can facilitate the horizontal transfer of antibiotic resistance or other genes associated with virulence. After replicating and propagating in a host, all transposon copies become inactivated and are lost unless the transposon passes to a genome by starting a new life cycle with horizontal transfer. It is important to note that DNA transposons do not randomly insert themselves into the genome, but rather show preference for specific sites.

<span class="mw-page-title-main">Jelly roll fold</span> Type of beta barrel protein domain structure

The jelly roll or Swiss roll fold is a protein fold or supersecondary structure composed of eight beta strands arranged in two four-stranded sheets. The name of the structure was introduced by Jane S. Richardson in 1981, reflecting its resemblance to the jelly or Swiss roll cake. The fold is an elaboration on the Greek key motif and is sometimes considered a form of beta barrel. It is very common in viral proteins, particularly viral capsid proteins. Taken together, the jelly roll and Greek key structures comprise around 30% of the all-beta proteins annotated in the Structural Classification of Proteins (SCOP) database.

<i>Ortervirales</i> Order of viruses

Ortervirales is an order that contains all accepted species of single-stranded RNA viruses that replicate through a DNA intermediate and all accepted species of double-stranded DNA viruses that replicate through an RNA intermediate . The name is derived from the reverse of retro.

<i>Riboviria</i> Realm of viruses

Riboviria is a realm of viruses that includes all viruses that use a homologous RNA-dependent polymerase for replication. It includes RNA viruses that encode an RNA-dependent RNA polymerase, as well as reverse-transcribing viruses that encode an RNA-dependent DNA polymerase. RNA-dependent RNA polymerase (RdRp), also called RNA replicase, produces RNA from RNA. RNA-dependent DNA polymerase (RdDp), also called reverse transcriptase (RT), produces DNA from RNA. These enzymes are essential for replicating the viral genome and transcribing viral genes into messenger RNA (mRNA) for translation of viral proteins.

In virology, realm is the highest taxonomic rank established for viruses by the International Committee on Taxonomy of Viruses (ICTV), which oversees virus taxonomy. Six virus realms are recognized and united by specific highly conserved traits:

<i>Monodnaviria</i> Realm of viruses

Monodnaviria is a realm of viruses that includes all single-stranded DNA viruses that encode an endonuclease of the HUH superfamily that initiates rolling circle replication of the circular viral genome. Viruses descended from such viruses are also included in the realm, including certain linear single-stranded DNA (ssDNA) viruses and circular double-stranded DNA (dsDNA) viruses. These atypical members typically replicate through means other than rolling circle replication.

<i>Cressdnaviricota</i> Phylum of viruses

Cressdnaviricota is a phylum of viruses with small, circular single-stranded DNA genomes and encoding rolling circle replication-initiation proteins with the N-terminal HUH endonuclease and C-terminal superfamily 3 helicase domains. While the replication-associated proteins are homologous among viruses within the phylum, the capsid proteins are very diverse and have presumably been acquired from RNA viruses on multiple independent occasions. Nevertheless, all cressdnaviruses for which structural information is available appear to contain the jelly-roll fold.

<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.

<i>Bamfordvirae</i> Kingdom of viruses

Bamfordvirae is a kingdom of viruses. This kingdom is recognized for its use of double jelly roll major capsid proteins. It was formerly known as the PRD1-adenovirus lineage. The kingdom is named after Dennis H. Bamford who first promoted the evolutionary unity of all viruses encoding double jelly-roll major capsid proteins.

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.

References

  1. 1 2 3 4 Kapitonov, V. V.; Jurka, J. (14 March 2006). "Self-synthesizing DNA transposons in eukaryotes". Proceedings of the National Academy of Sciences. 103 (12): 4540–4545. Bibcode:2006PNAS..103.4540K. doi: 10.1073/pnas.0600833103 . PMC   1450207 . PMID   16537396.
  2. 1 2 3 Pritham, Ellen J.; Putliwala, Tasneem; Feschotte, Cédric (April 2007). "Mavericks, a novel class of giant transposable elements widespread in eukaryotes and related to DNA viruses". Gene. 390 (1–2): 3–17. doi:10.1016/j.gene.2006.08.008. PMID   17034960.
  3. 1 2 3 4 5 6 7 8 Krupovic, Mart; Koonin, Eugene V. (22 December 2014). "Polintons: a hotbed of eukaryotic virus, transposon and plasmid evolution". Nature Reviews Microbiology. 13 (2): 105–115. doi:10.1038/nrmicro3389. PMC   5898198 . PMID   25534808.
  4. 1 2 Yutin, Natalya; Shevchenko, Sofiya; Kapitonov, Vladimir; Krupovic, Mart; Koonin, Eugene V. (11 November 2015). "A novel group of diverse Polinton-like viruses discovered by metagenome analysis". BMC Biology. 13 (1): 95. doi: 10.1186/s12915-015-0207-4 . PMC   4642659 . PMID   26560305.
  5. 1 2 3 4 Krupovic, Mart; Koonin, Eugene V (June 2016). "Self-synthesizing transposons: unexpected key players in the evolution of viruses and defense systems". Current Opinion in Microbiology. 31: 25–33. doi:10.1016/j.mib.2016.01.006. PMC   4899294 . PMID   26836982.
  6. 1 2 3 4 Haapa-Paananen, Saija; Wahlberg, Niklas; Savilahti, Harri (September 2014). "Phylogenetic analysis of Maverick/Polinton giant transposons across organisms". Molecular Phylogenetics and Evolution. 78: 271–274. doi:10.1016/j.ympev.2014.05.024. PMID   24882428.
  7. 1 2 Krupovic, Mart; Bamford, Dennis H; Koonin, Eugene V (2014). "Conservation of major and minor jelly-roll capsid proteins in Polinton (Maverick) transposons suggests that they are bona fide viruses". Biology Direct. 9 (1): 6. doi: 10.1186/1745-6150-9-6 . PMC   4028283 . PMID   24773695.
  8. 1 2 Yutin, Natalya; Raoult, Didier; Koonin, Eugene V (2013). "Virophages, polintons, and transpovirons: a complex evolutionary network of diverse selfish genetic elements with different reproduction strategies". Virology Journal. 10 (1): 158. doi: 10.1186/1743-422X-10-158 . PMC   3671162 . PMID   23701946.
  9. ↑ Dupuy, C.; Periquet, G.; Serbielle, C.; Bézier, A.; Louis, F.; Drezen, J-M (31 March 2011). "Transfer of a chromosomal Maverick to endogenous bracovirus in a parasitoid wasp". Genetica. 139 (4): 489–496. doi:10.1007/s10709-011-9569-x. PMID   21451967. S2CID   20901926.
  10. ↑ Koonin EV, Dolja VV, Krupovic M, Varsani A, Wolf YI, Yutin N, Zerbini M, Kuhn JH (October 2019). "Create a megataxonomic framework, filling all principal taxonomic ranks, for DNA viruses encoding vertical jelly roll-type major capsid proteins". ICTV Proposal (Taxoprop): 2019.003G. doi:10.13140/RG.2.2.14886.47684.
  11. ↑ Gao, X; Voytas, D (March 2005). "A eukaryotic gene family related to retroelement integrases". Trends in Genetics. 21 (3): 133–137. doi:10.1016/j.tig.2005.01.006. PMID   15734571.
  12. ↑ Feschotte, C; Pritham, E (October 2005). "Non-mammalian c-integrases are encoded by giant transposable elements". Trends in Genetics. 21 (10): 551–552. doi:10.1016/j.tig.2005.07.007. PMID   16084623.
This page is based on this Wikipedia article
Text is available under the CC BY-SA 4.0 license; additional terms may apply.
Images, videos and audio are available under their respective licenses.