Virus Rhizidiovirus

Rhizidiomyces virus
The Rhinovirus genus consists of dsRNA viruses[1] that infect stramenopiles.
Virology

The viron is non enveloped, isosahedral with a diameter of 60 nanometers (nm).

The genome is non segmented, linear double stranded DNA and ~25.5 kilobases in length. It has a guanine + cytosine content of 42%. It encodes at least 14 protein with molecular weights between 84.5 to 26 kiloDaltons.

The virus seems to remain latent within the host until the host is stressed. Virons first appear in the nucleus. This is followed by the disintegration of the host nucleus and cytoplasm and their replacement by paracrystalline structures composed of virons. These structures first appear in association with the mitochondria. After the nucleus and cytoplasm have been replaced the cell wall breaks down followed with release of virons into the medium. Vertical transmission also appears to be possible.
[edit] Literature

     Dawe VH, Kuhn CW (1983) Isolation and characterization of a double-stranded DNA mycovirus infecting the aquatic fungus, Rhizidiomyces. Virology 130(1):21-28
    Dawe VH, Kuhn CW (1983) Virus-like particles in the aquatic fungus, Rhizidiomyces.Virology 130(1):10-20.

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Virus Sputnik virophage

Sputnik virophage (from Russian cпутник "satellite", Latin "virus" and Greek φάγειν phagein "to eat") 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.

Viruses like Sputnik that depend on co-infection of the host cell by helper viruses are known as satellite viruses. At its discovery in a Paris water-cooling tower in 2008 Sputnik was the first known satellite virus that inhibited replication of its helper virus and thus acted as a parasite of that virus. In analogy to the term bacteriophage it was called a virophage.
Virology

Sputnik virophage is icosahedral in shape and 50 nanometres in size. It has been found to multiply inside of Acanthamoeba species, but only if that amoeba is infected with the large mamavirus. Sputnik harnesses the mamavirus proteins to rapidly produce new copies of itself.

Mamavirus is formally known as Acanthamoeba polyphaga mimivirus (APMV) and is a close relative of the previously known mimivirus. The mimivirus is a giant in the viral world; it has more genes than many bacteria and performs functions that normally occur only in cellular organisms. The mamavirus is even larger than the mimivirus, but the two are very similar in that they form large viral factories and complex viral particles.[2] Virophage growth is deleterious to APMV and results in the production of abortive forms and abnormal capsid assembly of APMV. In one of the experiments done by inoculating Acanthamoeba polyphaga with water containing an original strain of APMV, it was discovered that several capsid layers accumulate unsymmetrically on one side of the viral particle causing the virus to become ineffective. Sputnik decreased the yield of infective viral particle by 70% and also reduced the amoeba lysis by threefold at 24h.

Sputnik has a circular double stranded DNA genome consisting of 18,343 base pairs.[2] It contains genes able to infect all three domains of life: Eukarya, Archaea and Bacteria. Of the twenty-one predicted protein-coding genes, three are apparently derived from APMV itself, one is a homologue of an archaeal virus, and four others are homologues of proteins in bacteriophages and eukaryotic viruses. Thirteen are ORFans, that is they do not have any detectable homologues in current sequence databases. The Sputnik genome has a high A + T content (73%) similar to that of APMV.

Several other homologues such as those of a primase–helicase, a packaging ATPase, an insertion sequence transposase DNA-binding subunit, and a Zn-ribbon protein, were detected in the Global Ocean Survey environmental data set, suggesting that virophages could be a currently unknown family of viruses.

Sputnik was found to contain genes that were shared by APMV. These genes could have been acquired by Sputnik after the association of APMV with the host and then interaction between the virophage and the viral host. Recombination within the viral factory might have resulted in the exchange of genes. Sputnik is one of the most convincing pieces of evidence for gene mixing and matching between viruses.

The presence of these genes homologous to the mimivirus in Sputnik suggests that gene transfer between Sputnik and the mimivirus can occur during the infection of Acanthamoeba. Therefore, it is hypothesized that the virophage could be a source of vehicle mediating lateral gene transfer between giant viruses, which constitute a significant part of the DNA virus population in the marine environments. Moreover, the presence of three APMV genes in Sputnik implies that gene transfer between a virophage and a giant virus is crucial to viral evolution.

In March 2011, two additional virophages were described: the Mavirus virophage which preys on the giant Cafeteria roenbergensis virus, and the Organic Lake Virophage, found in the salty Organic Lake in Antarctica, and which preys on viruses that attack algae. All host viruses of the known virophages belong to the group of nucleocytoplasmic large DNA viruses.

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Virus Salterprovirus

The Salterprovirus is a genus of viruses that infect extremely halophilic archaea. The genus name is derived from salt terminal protein virus, as their linear dsDNA genomes have proteins attached to the 5' termini (i.e. terminal proteins). This virus morphotype is commonly observed in hypersaline waters around the world, and salterproviruses may represent an environmentally common halovirus.
Virology

The capsid is similar in shape to that of viruses infecting thermophilic Archaea, the Fuselloviridae, and His1 was originally described as a probable member of that group  However, it was later found that there is no genetic relationship and their replication strategies are entirely different, and so they were reclassified into a new group, Salterprovirus.

The genomes of His1 and His2 are similar in size (14,464 bp & 16,067 bp, respectively) and have the same number of predicted open reading frames (35), but they share almost no nucleotide sequence similarity. However, at the protein sequence level, their DNA polymerases share 42% identity. This, together with their similar morphologies, DNA structure (length, inverted terminal repeat sequences, terminal proteins), and mode of replication show that they belong to the same virus group.
A picture of His1 particles can be viewed at the www.haloarchaea.com website here, and scroll down. Curiously, homologues of the genes for the capsid proteins of His2 are widely distributed in genomes of haloarchaea[3]. The genomic loci containing these also tend to have other virus/plasmid genes nearby, and the term ViPREs  (for Virus and Plasmid Related Elements) has been proposed to denote these gene clusters, which may parallel the situation in thermophilic Archaea, where plasmids and viruses are closely linked.

Transfection of host cells (Haloarcula hispanica) by His2 DNA was demonstrated  who showed that infectious virus could be produced from viral DNA as long as the terminal proteins were not damaged by protease treatment. This is consistent with their likely role in DNA replication. It could then be shown that His2 DNA could transfect a wide variety of haloarchaeal species even though the cells were not susceptible to infection by His2 virus. In these experiments, transfected cells were plated along with cells of the host, Haloarcula hispanica, and virus produced by the transfectants was detected by infection of nearby cells of the susceptible host species. The experiments showed that the cytoplasms of many haloarchaea are able to replicate virus as long as the DNA (with terminal proteins) can enter. It is the virus capsid that determines cell selection, most likely by proteins in the short tail at one end of the spindle-shaped virion.

Once transfection had been established, it was possible to develop a system for mutagenesis, and the same publication described the use of an in vitro transposon system for inserting DNA randomly into the His2 genome. Transfection of the reaction products recovered virus recombinants with insertions, and mapping of these located regions of the His2 genome that were non-essential. Most insertions were found to lie in one of the two inverted terminal repeat (ITR) sequences. A few occurred at the very ends of three open reading frames. The study proved you could create His2 mutants, that you could insert at least 435 extra bp into the genome, and you could recover viable mutants with these insertions. This opens the way to analysing the functions of each of the virus genes, what they do and how they interact with each other and with the host cell. At present, almost all of the predicted virus proteins have no known function. It is not clear how much extra DNA can be inserted into the genome, but as is evident from the electronmicrograph, capsid size may not be a limiting factor, as the particle sizes of His1 vary considerably in length (and so probably for His2, although negative-stain EM of these particles is much more difficult).

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Virus Nudivirus

Nudiviruses are large and rod-shaped viruses with a circular, double stranded DNA genome. They are related to the baculoviruses and like these infect arthropods, particularly insects They share 20 core genes with baculoviruses. However, they are currently no longer regarded as members of the family Baculoviridae and are considered to be a sister group of these.
Taxonomy

In 2007, the genus Nudivirus has been proposed to include viruses similar to the Oryctes rhinoceros virus  Currently, the following viruses are considered to be members of the genus Nudivirus:

    Gryllus bimaculatus nudivirus (infecting the black cricket)
    Helicoverpa zea nudivirus 1 (infecting the cotton bollworm)
    Helicoverpa zea nudivirus 2 (infecting the cotton bollworm)
    Penaeus monodon nudivirus (infecting a shrimp)
    Oryctes rhinoceros nudivirus (infecting the rhinoceros beetle)

Properties

This genus is characterized by rod-shaped and enveloped nucleocapsids and its members replicate in the nucleus of infected host cells. However, the viruses are not embedded in inclusion bodies (crystallized proteins) like the baculoviruses. All sequenced nudiviruses have 33 open reading frames in common, 20 of them are homologous to baculovirus core genes involved in RNA transcription, DNA replication, virion structural components and other functions. Nudiviruses and baculoviruses appear to be derived from a common ancestor and evolutionarily related to other large DNA viruses
Relation to polydnaviruses in parasitic wasps


Parasitic wasps contain particles of polydnaviruses from portions of a nudivirus which have become part of the wasp genome. The genes help form particles like virions which are injected into the host larvae of the wasp and suppress a defensive response. The wasp eggs can then develop and parasitize the larva. 

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Virus Ampullavirus

The Ampullavirus consists of viruses that infect archaea. Ampulla means bottle in Latin, referring to the bottle-shape of the virion.
A DNA virus is a virus that has DNA as its genetic material and replicates using a DNA-dependent DNA polymerase. The nucleic acid is usually double-stranded DNA (dsDNA) but may also be single-stranded DNA (ssDNA). DNA viruses belong to either Group I or Group II of the Baltimore classification system for viruses. Single-stranded DNA is usually expanded to double-stranded in infected cells. Although Group VII viruses such as hepatitis B contain a DNA genome, they are not considered DNA viruses according to the Baltimore classification, but rather reverse transcribing viruses because they replicate through an RNA intermediate.

Virus classification is the process of naming viruses and placing them into a taxonomic system. Similar to the classification systems used for cellular organisms, virus classification is the subject of ongoing debate and proposals. This is mainly due to the pseudo-living nature of viruses, which are not yet definitively classified as living or non-living. As such, they do not fit neatly into the established biological classification system in place for cellular organisms.

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