Duplodnaviria
Duplodnaviria | |
---|---|
Illustrated sample of Duplodnaviria virions | |
Virus classification | |
(unranked): | Virus |
Realm: | Duplodnaviria |
Kingdom: | Heunggongvirae |
Subtaxa | |
Synonyms[1][2] | |
|
Duplodnaviria is a
Duplodnaviria was established in 2019 based on the shared characteristics of viruses in the realm. There are two groups of viruses in Duplodnaviria: tailed
Tailed bacteriophages are important in marine ecology by recycling nutrients in organic material from their hosts and are the focus of much research, and herpesviruses are associated with a variety of diseases in animals, including humans. A common feature among viruses in Duplodnaviria is that many are able to persist in their host for long periods of time without replicating while still being able to resurface in the future. Examples of this include the herpes simplex virus, which causes recurring infections, and the varicella zoster virus, which initially causes chickenpox early in life then shingles later in life.
Etymology
The name Duplodnaviria is a
Characteristics
All viruses in Duplodnaviria contain a distinct
After HK97 MCPs have been
A cylindrical opening in the capsid, called a portal, that serves as the entrance and exit for viral DNA is created with portal proteins at one of the 12 vertices of the capsid. The scaffold protein, which may be the delta domain of HK97 MCP, is removed from the inside of the capsid by the capsid maturation protease, which may also be a part of the scaffolding, breaking it and itself down to smaller molecules in a process called proteolysis that leaves the inside of the capsid empty.[3][4]
At the same time as capsid assembly, replication of the viral DNA occurs, creating concatemers, long molecules of DNA containing numerous copies of the viral genome. The enzyme terminase, made of two subunits, large and small, finds the viral DNA inside of the cell via the small subunit, cuts the concatemers, and creates the termini, or endings, of the genomes. Terminase recognizes a packaging signal in the genome and cuts the nucleic acid, creating a free end that it binds to.[3]
The terminase, now bound to the concatemer, attaches itself to the capsid portal and begins translocating the DNA from outside the capsid to the inside, using energy generated from ATP hydrolysis by the large subunit. As more DNA is inserted into the capsid, the capsid expands in size, becomes thinner, and its surface becomes flatter and more angular. Once the genome is completely inside, terminase cuts the concatemer again, completing packaging. Terminase then detaches itself from the portal and proceeds to repeat this process until all genomes in the concatemer have been packaged.[3]
For tailed bacteriophages, after DNA packaging, the tail of the virion, which was assembled separately, is attached to the capsid, commonly called the "head" of tailed bacteriophages, at the portal. Tailed bacteriophages also sometimes have "decoration" proteins that attach to the capsid's surface in order to reinforce the capsid's structure. After the virion is fully assembled inside the host cell, it leaves the cell.[3] Tailed bacteriophages leave the cell via lysis, rupturing of the cell membrane, that causes cell death,[5] and herpesviruses leave by budding from the host cell membrane, using the membrane as a viral envelope that covers the capsid.[6]
Phylogenetics
Tailed bacteriophages are potentially the oldest lineage of viruses in the world because they are ubiquitous worldwide, only infect prokaryotes, and have a high level of diversity. Their highly divergent virion structures may point to this or may indicate separate origins. The origin of Herpesvirales is unclear, but there are two likely scenarios. First, ancestral lineages of Caudoviricetes may have produced clades at various times that were capable of infecting eukaryotes, and the strong similarity that Herpesvirales has with Caudoviricetes may indicate that it is a more recent descendant of one such lineage. The second likely scenario is that Herpesvirales is a breakaway clade from within Caudoviricetes, which is supported by one of the Caudoviricetes subfamilies, Tevenvirinae, showing a relatively high genetic relation to herpesviruses based on certain protein amino acid sequences.[7] It has been suggested that Duplodnaviria predates the last universal common ancestor (LUCA) of cellular life and that viruses in the realm were present in the LUCA.[8]
The HK97 fold MCP appears to have been created from a
The ATPase subunit of Duplodnaviria terminases that generates energy for packaging viral DNA has the same general structural design of the P-loop fold as the packaging ATPases of double jelly roll fold MCP viruses in the realm Varidnaviria but are otherwise not directly related to each other. While viruses in Duplodnaviria make use of the HK97 fold for their major capsid proteins, the major capsid proteins of viruses in Varidnaviria instead are marked by single or double vertical jelly roll folds.[2]
Classification
Duplodnaviria contains only one kingdom, and this kingdom is subdivided into two phyla. This taxonomy can be visualized as follows:[10]
- Realm: Duplodnaviria
- Kingdom: Heunggongvirae
- Phylum: Peploviricota
- Class: Herviviricetes
- Order: Herpesvirales – the herpesviruses, which infect animals (eukaryotes)
- Phylum: Uroviricota
- Class: Caudoviricetes – the tailed bacteriophages, which infect archaea and bacteria (prokaryotes)
As all viruses in the realm are double-stranded DNA (dsDNA) viruses, the realm belongs to Group I: dsDNA viruses of Baltimore classification, a classification system based on a virus's manner of messenger RNA (mRNA) production, often used alongside standard virus taxonomy, which is based on evolutionary history.[2] Realms are the highest level of taxonomy used for viruses and Duplodnaviria is one of six, the other five being Adnaviria,Monodnaviria, Riboviria, Ribozyviria and Varidnaviria.[10]
Interactions with hosts
Viral shunt
Tailed bacteriophages are ubiquitous worldwide and are a major cause of death among prokaryotes. Infection may lead to cell death via lysis, the rupturing of the cell membrane. As a result of lysis, organic material from the killed prokaryotes is released into the environment, contributing to a process called viral shunt. Tailed bacteriophages shunt nutrients from organic material away from higher trophic levels so that they can be consumed by organisms in lower trophic levels, which has the effects of recycling nutrients and promoting increased diversity among marine life.[11]
Disease
Herpesviruses are associated with a wide range of diseases in their hosts, including
Latency
Viruses in Duplodnaviria have two different types of replication cycles, called the lytic cycle, whereby infection leads directly to virion formation and exit from the host cell, and the lysogenic cycle, whereby a latent infection retains the viral DNA inside of the host cell without virion formation, either as an episome or via integration into the host cell's DNA, with the possibility of returning to the lytic cycle in the future. Viruses that can replicate through the lysogenic cycle are called temperate or lysogenic viruses. Tailed bacteriophages vary in their temperateness, whereas all herpesviruses are temperate and able to avoid detection by the host's immune system, causing lifelong infections.[20][21]
History
Tailed bacteriophages were discovered independently by Frederick Twort in 1915 and Félix d'Hérelle in 1917, and they have been the focus of much research since then.[22] Diseases in humans caused by herpesviruses have been recognized for much of recorded history, and person-to-person transmission of the herpes simplex virus, the first herpesvirus discovered, was first recognized in 1893 by Émile Vidal.[23][24]
Over time, the two groups were increasingly found to share many characteristics, and their genetic relation was formalized with the establishment of Duplodnaviria in 2019. The creation of the kingdom, phyla, and classes of the realm in the same year has also created a framework to more easily allow major reorganization of Caudovirales, which is growing in size significantly and which may require tailed bacteriophages to be promoted to the rank of class or higher.[2]
See also
References
- ^ PMID 25864106.
- ^ a b c d e f Koonin EV, Dolja VV, Krupovic M, Varsani A, Wolf YI, Yutin N, Zerbini M, Kuhn JH (18 October 2019). "Create a megataxonomic framework, filling all principal/primary taxonomic ranks, for dsDNA viruses encoding HK97-type major capsid proteins" (docx). International Committee on Taxonomy of Viruses. Retrieved 19 May 2020.
- ^ PMID 26958920.
- ^ PMID 23688818.
- ^ "Myoviridae". ViralZone. Swiss Institute of Bioinformatics. Retrieved 19 May 2020.
- ^ "Herpesviridae". ViralZone. Swiss Institute of Bioinformatics. Retrieved 19 May 2020.
- PMID 31383901.
- ^ S2CID 220516514.
- PMID 28265094.
- ^ a b "Virus Taxonomy: 2019 Release". talk.ictvonline.org. International Committee on Taxonomy of Viruses. Retrieved 25 April 2020.
- JSTOR 1313569.
- PMID 17296156.
- PMID 23916092.
- PMID 27256025. Retrieved 15 June 2020.
- S2CID 7414402.
- PMID 27188665.
- PMID 9208806.
- PMID 27106239.
- PMID 31396258.
- PMID 32075270.
- ^ "Virus latency". ViralZone. Swiss Institute of Bioinformatics. Retrieved 15 June 2020.
- PMID 25521633.
- ISBN 978-3-642-84906-0.
- ^ Wildy P (1973) Herpes: history and classification. In: Kaplan AS, ed. The herpes-viruses. New York: Academic Press: 1-25. Accessed 15 June 2020.
Further reading
- Ward CW (1993). "Progress towards a higher taxonomy of viruses". Research in Virology. 144 (6): 419–53. PMID 8140287.