Duplodnaviria

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Duplodnaviria
Duplodnaviria virion morphology.jpg

Illustrated examples of virus particles of Duplodnaviria .
From left to right: Sipho- , Myo- and Podoviridae ,
as well as Herpesvirales

Systematics
Classification : Viruses
Area : Duplodnaviria
Taxonomic characteristics
Genome : dsDNA
Baltimore : Group 1
Symmetry : icosahedral
Scientific name
Duplodnaviria
Left
NCBI  Taxonomy: 2731341

Duplodnaviria is a range of viruses , all double-stranded DNA viruses comprises the major capsid protein ( English major capsid protein ) hk94 (HK97-MCP) encoding . This group was previously named HK97-like group or HK97 major capsid protein supermodule .

The members of this area also have a number of other proteins working together on the structure and the structure of the viral capsid with icosahedral involved form. Besides the capsid with HK97-MCP itself, these are the portal proteins. They form the opening of the capsid through which the DNA (when the virus particles are assembled) enters and exits (when the host cell is infected ). A Kapsidreifungsprotease ( English capsid maturation protease ) empties the inside of the capsid, before viral DNA is injected into the host cell, and a terminase - enzyme adds the viral DNA, a link assembly in the capsid to complete virus particles ( virions ) assemble.

In the area of Duplodnaviria there is only one sub taxon , the kingdom of Heunggongvirae . This has two phyla , each of which is monotypical up to the rank of order (as of April 2020). Therefore, there are currently only two orders of the Duplodnaviria , the Caudovirales ( bacteriophages with a head-tail structure that only infect prokaryotes - bacteria and archaea ) and the Herpesvirales (herpes viruses in the broader sense that only infect eukaryotes ).

Caudovirales are ubiquitous and very diverse worldwide, which is why their representatives are possibly among the oldest viruses of all. Probably the herpes viruses either come from a common ancestor with the caudovirales , if this has produced a lineage ( clade ) in its evolution that could infect eukaryotes; or they stem from a divergent branch within the caudovirales .

The relationship between caudovirales and herpes viruses has been known for a long time. The International Committee on Taxonomy of Viruses (ICTV) took this into account in 2019 by recognizing the Duplodnaviria division . The first part of the name (duplo) comes from Latin and means double ; the middle part (dna) relates to deoxyribonucleic acid (DNA), since all members of the range are double-stranded DNA viruses (dsDNA); and the last part (viria) is the suffix for virus areas. As dsDNA viruses, the members of this area all belong to Baltimore Group I (dsDNA viruses).

The Baltimore classification is based on the manner in which the viral messenger RNA ( mRNA ) is generated and is often used in conjunction with the standard virus taxonomy , which is based on evolutionary history and thus relationships. In the viral taxonomy, areas are the highest level (rank), and Duplodnaviria is one of currently (as of April 2020) four such areas; the others are Monodnaviria , Varidnaviria (both also contain DNA viruses) and Riboviria (the only area with RNA viruses including reverse transcribing viruses like the retroviruses ). However, a number of virus taxa have not yet been assigned to any areas.

construction

All viruses of the Duplodnaviria have an icosahedral capsid , which consists of a main capsid protein with a specific folded structure, which is called HK97 fold and is named after the HK97 main capsid protein (HK97-MCP) of the phage species Escherichia virus HK97 . Despite significant differences within the Duplodnaviria , the basic structure of the protein is retained (conserved) in all species in this area. Other common proteins responsible for the structure and assembly of the capsids include:

  • a portal protein that makes up the opening of the capsid,
  • a protease that empties the capsid before inserting DNA
  • the terminase enzyme, which inserts the DNA into the capsid.

Virus replication

After HK97-MCP has been synthesized by the host cell's ribosomes , the virus capsid is assembled by binding the proteins together. The interior of the capsid contains scaffold proteins ( English scaffold proteins ), which control the construction of the capsid in its geometric shape (the so-called. Assembly). In the absence of separate scaffold proteins, the delta domain of HK97-MCP, which points to the inside of the capsid, acts as a scaffold protein instead.

Then a cylindrical opening is formed in the capsid, which serves as an entrance and exit for viral DNA, and is therefore called a portal. The portal therefore corresponds in its function to the so-called Stargate , as can be found in some giant DNA viruses (e.g. mimivirus ). The portal is created with portal proteins at one of the 12 corner points of the capsid. The scaffold protein (if the domain of Delta HK97-MCP) is from the inside of the capsid through a capsid maturation protease ( English capsid maturation protease away), which can also be a part of the framework. This breaks up the scaffold protein (possibly itself) into smaller molecules ( proteolysis ) so that an empty capsid remains. In the case of herpes viruses, the protease is also known as assemblin .

Simultaneously with the capsid assembly, the replication of the viral DNA takes place , whereby concat a mere ( English concat e mer ) arise, i. H. long DNA molecules that contain numerous copies of the viral genome. An enzyme called terminase, consisting of a large and a small subunit, finds the viral DNA within the cell via its small subunit, cuts the concatamers and creates the ends of the genome (called termini, plural of terminus). The terminase recognizes a packaging signal in the genome (as a special DNA sequence) and cuts the nucleic acid, creating a free end to which it binds.

The terminase now bound to the concatamer, then binds to the capsid portal and begins to move the DNA from outside the capsid to the inside. This process consumes energy, which by virtue of an ATP - hydrolysis is produced by the large subunit. The more DNA is inserted into the capsid, the more the capsid expands, making it thinner and its surface increasingly approximating the icosahedral shape. Once the genome is completely inside, the terminase cuts off the concatamer again, completing the packaging process. The terminase then detaches from the portal and repeats this process until all of the concatamer's DNA genomes are packaged.

In the case of bacteriophages with a head-to-tail structure ( caudovirales ), after DNA packaging, the tail of the virion, which was previously assembled separately, is bound to the capsid at the portal, which is then usually referred to as the head in this virus type. With these viruses one can sometimes also find so-called decoration proteins, which attach to the surface of the capsid in order to strengthen the structure of the capsid.

After the virion is fully assembled in the host cell, it leaves the cell.

  • Tail bacteriophage leave the cell by lysis ; H. Breaking the cell membrane, which leads to cell death.
  • Herpes viruses occur by budding ( English budding ) from the host cell membrane out, said membrane material is used as a viral envelope, which covers the capsid.

etiology

In the tail phage, infection usually leads to cell death of the host bacterium or archaeon. However, herpes viruses cause a variety of diseases in their hosts. In humans, diseases caused by herpes viruses include herpes simplex , chickenpox, and shingles (herpes zoster), roseola (three-day fever), and various cancers such as lymphoma , nasopharyngeal carcinoma, and Kaposi's sarcoma . Herpes viruses are also known to evade the immune system and cause a latent infection that can last for long periods of time. Examples include the varicella zoster virus , which typically causes chickenpox early in life and often decades later, causing herpes zoster.

Systematics

The area Duplodnaviria currently (as of April 2020) contains only a single kingdom Heunggongvirae , which is divided into two phyla , which are monotypical up to the rank of order, i.e. H. each contain only one order:

  • Area: Duplodnaviria
  • Empire: Heunggongvirae
  • Phylum: Peploviricota
  • Class: Herviviricetes
  • Phylum: Uroviricota
  • Class: Caudoviricetes

Development history

Head-to-tail phages are possibly the oldest line of viruses in the world:

  • they are ubiquitous all over the world
  • they only infect prokaryotes - eukaryotes probably developed later from a branch of the (prokaryotic) archaea, see eocyte hypothesis )
  • they have a high degree of diversity.

The strongly diverging virion structures could also point to different origins. The origin of herpes viral is unclear, but there are two likely scenarios:

  1. The caudovirales could at different times have produced lineages capable of infecting eukaryotes. The close resemblance between the herpesvirales and the caudovirales could indicate that it is these recent descendants of such a line.
  2. The second possible scenario is that the herpes viruses are a highly developed 'runaway' clade from within the caudovirals . This is supported by the fact that some families of the caudovirales , such as the Myoviridae (and especially their subfamily Tevenvirinae , show a relatively high similarity to herpes viruses on the basis of certain amino acid sequences of their proteins ( proteome )

The ATPase subunit of the Duplodnaviria terminases , which generates energy to package the viral DNA, has the same general structural design of a P-loop fold (also called Walker motif ) as the packaging ATPases from the DJR viruses of the Varidnaviria region ( English double jelly roll fold ); however, they are not otherwise directly related to each other. While the Duplodnaviria viruses use the HK97 fold for their main capsid proteins, the main capsid proteins in the Varidnaviria are instead characterized by single or double vertical jelly roll folds.


Individual evidence

  1. ↑ ICTV: ICTV Taxonomy history: Human alphaherpesvirus 1 , EC 51, Berlin, Germany, July 2019; Email ratification March 2020 (MSL # 35)
  2. ↑ a b c d e f g Eugen V. Koonin, V. V. Dolja, M. Krupovic, A. Varsani, Y. I. Wolf, N. Yutin, M. Zerbini, J. H. Kuhn: Create a megataxonomic framework, filling all principal / primary taxonomic ranks , for dsDNA viruses encoding HK97-type major capsid proteins ( en , docx) October 18, 2019.
  3. ↑ a b c M. M. Suhanovsky, C. M. Teschke: Nature's favorite building block: Deciphering folding and capsid assembly of proteins with the HK97-fold . In: Virology . 479-480, May 2015, pp. 479-480. doi : 10.1016 / j.virol.2015.02.055 . PMID 25864106 . PMC 4424165 (free full text).
  4. ↑ a b c R. I. Duda, B. Oh, R. W. Hendrix: Functional domains of the HK97 capsid maturation protease and the mechanisms of protein encapsidation . In: J Mol Biol . 425, No. 15, August 9, 2013, pp. 2765-2781. doi : 10.1016 / j.jmb.2013.05.002 . PMID 23688818 . PMC 3709472 (free full text).
  5. ↑ a b c Virus Taxonomy: 2019 Release . International Committee on Taxonomy of Viruses.
  6. ^ A b J. S. Andrade-Martínez, J. L. Moreno-Gallego, A. Reyes: Defining a Core Genome for the Herpesvirales and Exploring their Evolutionary Relationship with the Caudovirales . In: Sci Rep . 9, No. 1, August 2019, p. 11342. bibcode : 2019NatSR ... 911342A . doi : 10.1038 / s41598-019-47742-z . PMID 31383901 . PMC 6683198 (free full text).
  7. ↑ a b c d e f V. B. Rao, M. Feiss: Mechanisms of DNA Packaging by Large Double-Stranded DNA Viruses . In: Annu Rev Virol . 2, No. 1, November 2015, pp. 351–378. doi : 10.1146 / annurev-virology-100114-055212 . PMID 26958920 . PMC 4785836 (free full text).
  8. ↑ Myoviridae . Swiss Institute of Bioinformatics. Retrieved May 19, 2020.
  9. ↑ a b Herpesviridae . Swiss Institute of Bioinformatics. Retrieved May 19, 2020.

literature