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33-406: Circoviridae is a family of DNA viruses . Birds and mammals serve as natural hosts. There are 101 species in this family, assigned to 2 genera. Diseases associated with this family include: PCV-2: postweaning multisystemic wasting syndrome ; CAV: chicken infectious anemia. Viruses in the family Circoviridae are non-enveloped, with icosahedral and round geometries, and T=1 symmetry. The diameter

66-410: A jelly roll fold folded structure in which the jelly roll (JR) fold is perpendicular to the surface of the viral capsid. Many members also share a variety of other characteristics, including a minor capsid protein that has a single JR fold, an ATPase that packages the genome during capsid assembly, and a common DNA polymerase . Two kingdoms are recognized: Helvetiavirae , whose members have MCPs with

99-569: A TFIIE homolog, which assists in transcription initiation but is not required. Formation of the Pol I preinitiation complex requires the binding of selective factor 1 (SL1 or TIF-IB) to the core element of the rDNA promoter. SL1 is a complex composed of TBP and at least three TBP-associated factors (TAFs). For basal levels of transcription, only SL1 and the initiation-competent form of Pol I (Pol Iβ), characterized by RRN3 binding, are required. For activated transcription levels, UBTF (UBF)

132-414: A consequence of replication of the viral genome. Eukaryotic ssDNA viruses are replicated in the nucleus. Most ssDNA viruses contain circular genomes that are replicated via rolling circle replication (RCR). ssDNA RCR is initiated by an endonuclease that bonds to and cleaves the positive strand, allowing a DNA polymerase to use the negative strand as a template for replication. Replication progresses in

165-416: A dsDNA genome. Lastly, some dsDNA viruses are replicated as part of a process called replicative transposition whereby a viral genome in a host cell's DNA is replicated to another part of a host genome. dsDNA viruses can be subdivided between those that replicate in the cell nucleus , and as such are relatively dependent on host cell machinery for transcription and replication, and those that replicate in

198-461: A few exceptions and peculiarities exist. The family Anelloviridae is the only ssDNA family whose members have negative sense genomes, which are circular. Parvoviruses, as previously mentioned, may package either the positive or negative sense strand into virions. Lastly, bidnaviruses package both the positive and negative linear strands. The International Committee on Taxonomy of Viruses (ICTV) oversees virus taxonomy and organizes viruses at

231-527: A loop around the genome by means of extending the 3'-end of the positive strand, displacing the prior positive strand, and the endonuclease cleaves the positive strand again to create a standalone genome that is ligated into a circular loop. The new ssDNA may be packaged into virions or replicated by a DNA polymerase to form a double-stranded form for transcription or continuation of the replication cycle. Parvoviruses contain linear ssDNA genomes that are replicated via rolling hairpin replication (RHR), which

264-534: A major capsid protein (MCP) that has the HK97 fold. Viruses in the realm also share a number of other characteristics involving the capsid and capsid assembly, including an icosahedral capsid shape and a terminase enzyme that packages viral DNA into the capsid during assembly. Two groups of viruses are included in the realm: tailed bacteriophages, which infect prokaryotes and are assigned to the order Caudovirales , and herpesviruses, which infect animals and are assigned to

297-445: A manner similar to the bacterial RNA polymerase (RNAP). Archaea have a preinitiation complex resembling that of a minimized Pol II PIC, with a TBP and an Archaeal transcription factor B (TFB, a TFIIB homolog). The assembly follows a similar sequence, starting with TBP binding to the promoter. An interesting aspect is that the entire complex is bound in an inverse orientation compared to those found in eukaryotic PIC. They also use TFE,

330-541: A possible animal reservoir. DNA virus 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

363-461: A realm: ssDNA viruses are classified into one realm and include several families that are unassigned to a realm: Transcription preinitiation complex The minimal PIC includes RNA polymerase II and six general transcription factors : TF II A , TF II B , TF II D , TF II E , TF II F , and TF II H . Additional regulatory complexes (such as the mediator coactivator and chromatin remodeling complexes) may also be components of

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396-565: A relation to a group of proteins that contain SJR folds, including the Cupin superfamily and nucleoplasmins . Marine viruses in Varidnaviria are ubiquitous worldwide and, like tailed bacteriophages, play an important role in marine ecology. Most identified eukaryotic DNA viruses belong to the realm. Notable disease-causing viruses in Varidnaviria include adenoviruses , poxviruses , and

429-418: A replication origin site and move in opposite directions of each other, is widely used. A rolling circle mechanism that produces linear strands while progressing in a loop around the circular genome is also common. Some dsDNA viruses use a strand displacement method whereby one strand is synthesized from a template strand, and a complementary strand is then synthesized from the prior synthesized strand, forming

462-460: A single vertical JR fold, and Bamfordvirae , whose members have MCPs with two vertical JR folds. Varidnaviria is either monophyletic or polyphyletic and may predate the LUCA. The kingdom Bamfordvirae is likely derived from the other kingdom Helvetiavirae via fusion of two MCPs to have an MCP with two jelly roll folds instead of one. The single jelly roll (SJR) fold MCPs of Helvetiavirae show

495-401: A single-stranded DNA genome. ssDNA viruses have the same manner of transcription as dsDNA viruses. However, because the genome is single-stranded, it is first made into a double-stranded form by a DNA polymerase upon entering a host cell. mRNA is then synthesized from the double-stranded form. The double-stranded form of ssDNA viruses may be produced either directly after entry into a cell or as

528-539: Is also required. UBTF binds as a dimer to both the upstream control element (UCE) and core element of the rDNA promoter, bending the DNA to form an enhanceosome . SL1 has been found to stabilize the binding of UBTF to the rDNA promoter. The subunits of the Pol I PIC differ between organisms. Pol III has three classes of initiation, which start with different factors recognizing different control elements but all converging on TFIIIB (similar to TFIIB-TBP; consists of TBP/TRF,

561-425: Is around 20 nm. Genomes are circular and non-segmented, around 3.8kb in length. The capsid consists of 12 pentagonal trumpet-shaped pentamers. There are two main open reading frames arranged in opposite directions that encode the replication and capsid proteins . Alternative start codons are common in the avian species. Viral replication is nuclear. Entry into the host cell is achieved by penetration into

594-433: Is chiefly based on transcription of mRNA, viruses in each Baltimore group also typically share their manner of replication. Viruses in a Baltimore group do not necessarily share genetic relation or morphology. The first Baltimore group of DNA viruses are those that have a double-stranded DNA genome. All dsDNA viruses have their mRNA synthesized in a three-step process. First, a transcription preinitiation complex binds to

627-436: Is not fully understood. The relation between caudoviruses and herpesviruses is also uncertain: they may share a common ancestor or herpesviruses may be a divergent clade from the realm Caudovirales . A common trait among duplodnaviruses is that they cause latent infections without replication while still being able to replicate in the future. Tailed bacteriophages are ubiquitous worldwide, important in marine ecology, and

660-552: Is similar to RCR. Parvovirus genomes have hairpin loops at each end of the genome that repeatedly unfold and refold during replication to change the direction of DNA synthesis to move back and forth along the genome, producing numerous copies of the genome in a continuous process. Individual genomes are then excised from this molecule by the viral endonuclease. For parvoviruses, either the positive or negative sense strand may be packaged into capsids, varying from virus to virus. Nearly all ssDNA viruses have positive sense genomes, but

693-489: The African swine fever virus . Poxviruses have been highly prominent in the history of modern medicine, especially Variola virus , which caused smallpox . Many varidnaviruses can become endogenized in their host's genome; a peculiar example are virophages , which after infecting a host, can protect the host against giant viruses . dsDNA viruses are classified into three realms and include many taxa that are unassigned to

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726-441: The cytoplasm , in which case they have evolved or acquired their own means of executing transcription and replication. dsDNA viruses are also commonly divided between tailed dsDNA viruses, referring to members of the realm Duplodnaviria , usually the tailed bacteriophages of the order Caudovirales , and tailless or non-tailed dsDNA viruses of the realm Varidnaviria . The second Baltimore group of DNA viruses are those that have

759-553: The DNA upstream of the site where transcription begins, allowing for the recruitment of a host RNA polymerase . Second, once the RNA polymerase is recruited, it uses the negative strand as a template for synthesizing mRNA strands. Third, the RNA polymerase terminates transcription upon reaching a specific signal, such as a polyadenylation site. dsDNA viruses make use of several mechanisms to replicate their genome. Bidirectional replication, in which two replication forks are established at

792-480: The PIC. Preinitiation complexes are also formed during RNA Polymerase I and RNA Polymerase III transcription. A classical view of PIC formation at the promoter involves the following steps: An alternative hypothesis of PIC assembly postulates the recruitment of a pre-assembled " RNA polymerase II holoenzyme " directly to the promoter (composed of all, or nearly all GTFs and RNA polymerase II and regulatory complexes), in

825-611: The basal level at the rank of realm. Virus realms correspond to the rank of domain used for cellular life but differ in that viruses within a realm do not necessarily share common ancestry , nor do the realms share common ancestry with each other. As such, each virus realm represents at least one instance of viruses coming into existence. Within each realm, viruses are grouped together based on shared characteristics that are highly conserved over time. Three DNA virus realms are recognized: Duplodnaviria , Monodnaviria , and Varidnaviria . Duplodnaviria contains dsDNA viruses that encode

858-446: The host cell. Replication follows the ssDNA rolling circle model. DNA templated transcription, with some alternative splicing mechanism is the method of transcription. The virus exits the host cell by nuclear egress, and nuclear pore export. A stem loop structure with a conserved nonanucleotide motif is located at the 5' intergenic region of circovirus genomes and is thought to initiate rolling-cycle replication. Birds and mammals serve as

891-445: The natural host. Transmission routes are fecal-oral. The family Circoviridae contains two genera— Circovirus and Cyclovirus . A cyclovirus— cyclovirus-Vietnam —has been isolated from the cerebrospinal fluid of 25 Vietnamese patients with CNS infections of unknown aetiology. The same virus has been isolated from the faeces of healthy children and also from pigs and chickens. This suggests an orofaecal route of transmission with

924-519: The order Herpesvirales . Duplodnaviria is a very ancient realm, perhaps predating the last universal common ancestor (LUCA) of cellular life. Its origins not known, nor whether it is monophyletic or polyphyletic. A characteristic feature is the HK97-fold found in the MCP of all members, which is found outside the realm only in encapsulins , a type of nanocompartment found in bacteria: this relation

957-550: The origins of Duplodnaviria and Varidnaviria are less clear. Prominent disease-causing DNA viruses include herpesviruses , papillomaviruses , and poxviruses . The Baltimore classification system is used to group viruses together based on their manner of messenger RNA (mRNA) synthesis and is often used alongside standard virus taxonomy, which is based on evolutionary history. DNA viruses constitute two Baltimore groups: Group I: double-stranded DNA viruses, and Group II: single-stranded DNA viruses. While Baltimore classification

990-734: 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 . DNA viruses are ubiquitous worldwide, especially in marine environments where they form an important part of marine ecosystems, and infect both prokaryotes and eukaryotes . They appear to have multiple origins, as viruses in Monodnaviria appear to have emerged from archaeal and bacterial plasmids on multiple occasions, though

1023-447: The realm are called CRESS-DNA viruses and have circular ssDNA genomes. ssDNA viruses with linear genomes are descended from them, and in turn some dsDNA viruses with circular genomes are descended from linear ssDNA viruses. Viruses in Monodnaviria appear to have emerged on multiple occasions from archaeal and bacterial plasmids , a type of extra-chromosomal DNA molecule that self-replicates inside its host. The kingdom Shotokuvirae in

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1056-673: The realm likely emerged from recombination events that merged the DNA of these plasmids and complementary DNA encoding the capsid proteins of RNA viruses. CRESS-DNA viruses include three kingdoms that infect prokaryotes: Loebvirae , Sangervirae , and Trapavirae . The kingdom Shotokuvirae contains eukaryotic CRESS-DNA viruses and the atypical members of Monodnaviria . Eukaryotic monodnaviruses are associated with many diseases, and they include papillomaviruses and polyomaviruses , which cause many cancers, and geminiviruses , which infect many economically important crops. Varidnaviria contains DNA viruses that encode MCPs that have

1089-448: The subject of much research. Herpesviruses are known to cause a variety of epithelial diseases, including herpes simplex , chickenpox and shingles , and Kaposi's sarcoma . Monodnaviria contains ssDNA viruses that encode an endonuclease of the HUH superfamily that initiates rolling circle replication and all other viruses descended from such viruses. The prototypical members of

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