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46-496: Adnaviria is a realm of viruses that includes archaeal viruses that have a filamentous virion (i.e. body) and a linear, double-stranded DNA genome. The genome exists in A-form ( A-DNA ) and encodes a dimeric major capsid protein (MCP) that contains the SIRV2 fold, a type of alpha-helix bundle containing four helices. The virion consists of the genome encased in capsid proteins to form

92-572: A reverse transcriptase (RT), assigned to the kingdom Pararnavirae . These enzymes are vital in the viral life cycle, as RdRp transcribes viral mRNA and replicates the genome, and RT likewise replicates the genome. Riboviria mostly contains eukaryotic viruses, and most eukaryotic viruses, including most human, animal, and plant viruses, belong to the realm. Most widely known viral diseases are caused by viruses in Riboviria , which includes influenza viruses , HIV , coronaviruses , ebolaviruses , and

138-498: A family of filamentous archaeal viruses morphologically similar to adnaviruses, likewise possess MCPs that show no relation to the MCPs of viruses in Adnaviria and for that reason are excluded from the realm. Adnaviria is monotypic down to the rank of its sole class, Tokiviricetes , which has three orders. This taxonomy is shown hereafter: Viruses of Adnaviria began to be discovered in

184-402: A helical nucleoprotein complex containing genomic A-DNA. The nucleoprotein helix is composed of asymmetric units of two MCPs. For rudiviruses , this is a homodimer, whereas for lipothrixviruses and tristromaviruses , it is a heterodimer of paralogous MCPs. The MCPs of viruses in Adnaviria contain a folded structure consisting of a type of alpha-helix bundle that contains four helices called

230-421: A helical nucleoprotein complex. For some viruses, this helix is surrounded by a lipid membrane called an envelope . Some contain an additional protein layer between the nucleoprotein helix and the envelope. Complete virions are long and thin and may be flexible or a stiff like a rod. Adnaviria was established in 2020 after cryogenic electron microscopy showed that the viruses in the realm were related due to

276-479: A long time, as it is thought that they may have infected the last archaeal common ancestor. In general, they show no genetic relation to viruses outside the realm. The only genes that are shared with other viruses are glycosyltransferases , ribbon-helix-helix transcription factors , and anti- CRISPR proteins. Adnaviruses are morphologically similar to non-archaeal filamentous viruses but their virions are built from different capsid proteins. Viruses of Clavaviridae ,

322-530: 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

368-574: A new glycosyltransferase fold was identified for the glycosyltransferases involved in the biosynthesis of the NAG-NAM polymer backbone of peptidoglycan . Many inhibitors of glycosyltransferases are known. Some of these are natural products, such as moenomycin , an inhibitor of peptidoglycan glycosyltransferases, the nikkomycins , inhibitors of chitin synthase, and the echinocandins , inhibitors of fungal β-1,3-glucan synthases . Some glycosyltransferase inhibitors are of use as drugs or antibiotics. Moenomycin

414-540: A sequence-based classification of glycosyltransferases into over 90 families. The same three-dimensional fold is expected to occur within each of the families. In contrast to the diversity of 3D structures observed for glycoside hydrolases , glycosyltransferase have a much smaller range of structures. In fact, according to the Structural Classification of Proteins database, only three different folds have been observed for glycosyltransferases Very recently,

460-470: A shared MCP, A-DNA, and general virion structure. Viruses in Adnaviria infect hyperthermophilic archaea , i.e. archaea that inhabit very high temperature environments such as hot springs. Their A-DNA genome may be an adaptation to this extreme environment. Viruses in Adnaviria have potentially existed for a long time, as it is thought that they may have infected the last archaeal common ancestor. In general, they show no genetic relation to any viruses outside

506-456: A vast undescribed diversity of viruses in this part of the virosphere. Ribozyviria is characterised by the presence of genomic and antigenomic ribozymes of the Deltavirus type. Additional common features include a rod-like structure and a RNA-binding "delta antigen" encoded in the genome. In general, virus realms have no genetic relation to each other based on common descent, in contrast to

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552-657: Is an AB, A, B or O blood type. Glycosyltransferases have been widely used in both the targeted synthesis of specific glycoconjugates as well as the synthesis of differentially glycosylated libraries of drugs, biological probes or natural products in the context of drug discovery and drug development (a process known as glycorandomization ). Suitable enzymes can be isolated from natural sources or produced recombinantly. As an alternative, whole cell-based systems using either endogenous glycosyl donors or cell-based systems containing cloned and expressed systems for synthesis of glycosyl donors have been developed. In cell-free approaches,

598-457: Is composed of asymmetric units containing two MCP molecules, a homodimer in the case of rudivirids and a heterodimer of paralogous MCPs in the case of lipothrixvirids and tristromavirids. The MCPs of ligamenviral particles have a unique α-helical fold first found in the MCP of rudivirid Sulfolobus islandicus rod-shaped virus 2 (SIRV2). All members of the Adnaviria share a characteristic feature in that

644-604: Is derived from Latin talea , meaning "rod", referring to the morphology of viruses in the realm, and the virus phylum suffix - viricota . Lastly, the sole class in the realm, Tokiviricetes , is constructed from Georgian toki (თოკი), meaning "thread", and the suffix used for virus classes, - viricetes . Viruses in Adnaviria infect hyperthermophilic archaea and have linear, double-stranded DNA (dsDNA) genomes ranging from about 16 to 56 kilobase pairs in length. The ends of their genomes contain inverted terminal repeats. Notably, their genomes exist in A-form, also called A-DNA. A-form

690-455: Is determined by what type of glycosyltransferases are expressed in the body. The ABO gene locus expressing the glycosyltransferases has three main allelic forms: A, B, and O. The A allele encodes 1-3-N-acetylgalactosaminyltransferase that bonds α- N-acetylgalactosamine to D-galactose end of H antigen, producing the A antigen. The B allele encodes 1-3-galactosyltransferase that joins α-D-galactose bonded to D-galactose end of H antigen, creating

736-465: Is proposed to be an adaptation allowing DNA survival under extreme conditions since their hosts are hyperthermophilic and acidophilic microorganisms from the archaea domain. Furthermore, Adnaviria viruses have high genome redundancy, an adaptation mechanism to survive such extreme environments. The creation of genomic A-DNA is caused by an interaction with major capsid protein (MCP) dimers, which, during virion assembly, cover pre-genomic B-DNA to form

782-431: Is relatively abundant in eukaryotes. Transferases may also use lipids as an acceptor, forming glycolipids , and even use lipid-linked sugar phosphate donors, such as dolichol phosphates in eukaryotic organism, or undecaprenyl phosphate in bacteria. Glycosyltransferases that use sugar nucleotide donors are Leloir enzymes , after Luis F. Leloir , the scientist who discovered the first sugar nucleotide and who received

828-555: Is surrounded by a lipid envelope. Tristromaviruses, about 400 by 32 nm, likewise have flexible virions with an envelope, and they contain an additional protein sheath layer between the nucleoprotein complex and the envelope. Rudviruses have stiff, rod-like virions about 600–900 by 23 nm. At both ends of the virion, lipothrixviruses have mop- or claw-like structures connected to a collar, whereas rudiviruses and tristromaviruses have plugs at each end from which bundles of thin filaments emanate. Viruses in Adnaviria have potentially existed for

874-510: Is used in animal feed as a growth promoter. Caspofungin has been developed from the echinocandins and is in use as an antifungal agent. Ethambutol is an inhibitor of mycobacterial arabinotransferases and is used for the treatment of tuberculosis. Lufenuron is an inhibitor of insect chitin syntheses and is used to control fleas in animals. Imidazolium -based synthetic inhibitors of glycosyltransferases have been designed for use as antimicrobial and antiseptic agents. The ABO blood group system

920-413: The rabies virus , as well as the first virus to be discovered, Tobacco mosaic virus . Reverse transcribing viruses are a major source of horizontal gene transfer by means of becoming endogenized in their host's genome, and a significant portion of the human genome consists of this viral DNA. Varidnaviria contains DNA viruses that encode MCPs that have a jelly roll fold folded structure in which

966-637: The " glycosyl donor ") to a nucleophilic glycosyl acceptor molecule, the nucleophile of which can be oxygen - carbon -, nitrogen -, or sulfur -based. The result of glycosyl transfer can be a carbohydrate , glycoside , oligosaccharide , or a polysaccharide . Some glycosyltransferases catalyse transfer to inorganic phosphate or water . Glycosyl transfer can also occur to protein residues, usually to tyrosine , serine , or threonine to give O-linked glycoproteins , or to asparagine to give N-linked glycoproteins. Mannosyl groups may be transferred to tryptophan to generate C-mannosyl tryptophan , which

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1012-874: The 1970 Nobel Prize in Chemistry for his work on carbohydrate metabolism. Glycosyltransferases that use non-nucleotide donors such as dolichol or polyprenol pyrophosphate are non-Leloir glycosyltransferases . Mammals use only 9 sugar nucleotide donors for glycosyltransferases: UDP-glucose , UDP-galactose , UDP-GlcNAc , UDP-GalNAc , UDP-xylose , UDP-glucuronic acid , GDP-mannose , GDP-fucose , and CMP-sialic acid . The phosphate(s) of these donor molecules are usually coordinated by divalent cations such as manganese, however metal independent enzymes exist. Many glycosyltransferases are single-pass transmembrane proteins , and they are usually anchored to membranes of Golgi apparatus Glycosyltransferases can be segregated into "retaining" or "inverting" enzymes according to whether

1058-467: The 1980s by Wolfram Zillig and his colleagues. To discover these viruses, Zillig developed the methods used to culture their hosts. The first of these to be described were TTV1, TTV2, and TTV3 in 1983. TTV1 was classified as the first lipothrixvirus but is now classified as a tristromavirus. SIRV2, a rudivirus, became a model for studying virus-host interactions after its discovery in 1998. The families Lipothrixviridae and Rudiviridae were then united under

1104-529: The B antigen. In case of O allele the exon 6 contains a deletion that results in a loss of enzymatic activity. The O allele differs slightly from the A allele by deletion of a single nucleotide - Guanine at position 261. The deletion causes a frameshift and results in translation of an almost entirely different protein that lacks enzymatic activity. This results in H antigen remaining unchanged in case of O groups. The combination of glycosyltransferases by both alleles present in each person determines whether there

1150-420: The SIRV2 fold, named after the virus of the same name, Sulfolobus islandicus rod-shaped virus 2 (SIRV2). Variations in the protein structure exist, but the same base structure is retained in all adnaviruses. Adnaviruses have filamentous virions, i.e. they are long, thin, and cylindrical. Lipothrixviruses have flexible virions about 900 nanometers (nm) in length and 24 nm in width in which the nucleoprotein helix

1196-412: The anomeric carbon for a net retention of stereochemistry) or a dissociative mechanism (a prevalent variant of which was known as SNi). An "orthogonal associative" mechanism has been proposed which, akin to the inverting enzymes, requires only a single nucleophilic attack from an acceptor from a non-linear angle (as observed in many crystal structures) to achieve anomer retention. The recent discovery of

1242-462: 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. Riboviria contains all RNA viruses that encode an RNA-dependent RNA polymerase (RdRp), assigned to the kingdom Orthornavirae , and all reverse transcribing viruses, i.e. all viruses that encode

1288-569: The desire to establish higher-level taxonomy for viruses. In two votes in 2018 and 2019, the ICTV agreed to adopt a 15-rank classification system for viruses, ranging from realm to species. Riboviria was established in 2018 based on phylogenetic analysis of the RNA-dependent polymerases being monophyletic, Duplodnaviria was established in 2019 based on increasing evidence that tailed bacteriophages and herpesviruses shared many traits, Monodnaviria

1334-470: The first part of Monodnaviria means "single DNA", referring to ssDNA viruses, the first part of Riboviria is taken from ribo nucleic acid (RNA), and the first part of Varidnaviria means "various DNA". For viroids , the suffix is designated as - viroidia , and for satellites , the suffix is - satellitia , but as of 2019 neither viroid nor satellite realms have been designated. Duplodnaviria contains double-stranded DNA (dsDNA) viruses that encode

1380-453: The interaction between the MCP dimer and the linear dsDNA genome maintains the DNA in the A form. Consequently, the entire genome adopts the A form in virions. Like many structurally related viruses in the two other realms of dsDNA viruses ( Duplodnaviria and Varidnaviria ), there is no detectable sequence similarity among the capsid proteins of viruses from different tokiviricete families, suggesting

1426-705: 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 a single vertical JR fold, and Bamfordvirae , whose members have MCPs with two vertical JR folds. 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

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1472-421: The large-scale application of glycosyltransferases for glycoconjugate synthesis has required access to large quantities of the glycosyl donors. On the flip-side, nucleotide recycling systems that allow the resynthesis of glycosyl donors from the released nucleotide have been developed. The nucleotide recycling approach has a further benefit of reducing the amount of nucleotide formed as a by-product, thereby reducing

1518-496: The order Herpesvirales . The relation between caudoviruses and herpesviruses is not certain, as they may either share a common ancestor or herpesviruses may be a divergent clade from within 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

1564-670: The order Ligamenvirales in 2012 based on evidence of their relation. Cryogenic electron microscopy would later show in 2020 that the MCPs of tristromaviruses contained a SIRV2-like fold like ligamenviruses, providing justification for establishing Adnaviria in the same year. Realm (virology) 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: The rank of realm corresponds to

1610-480: The rank of domain used for cellular life, but differs in that viruses in a realm do not necessarily share a common ancestor based on common descent nor do the realms share a common ancestor . Instead, realms group viruses together based on specific traits that are highly conserved over time, which may have been obtained on a single occasion or multiple occasions. As such, each realm represents at least one instance of viruses coming into existence. While historically it

1656-612: The rank of subrealm. Prior to the 21st century, it was believed that deep evolutionary relations between viruses could not be discovered due to their high mutation rates and small number of genes making discovering these relations more difficult. Because of this, the highest taxonomic rank for viruses from 1991 to 2017 was order. In the 21st century, however, various methods have been developed that have enabled these deeper evolutionary relationships to be studied, including metagenomics, which has identified many previously unidentified viruses, and comparison of highly conserved traits, leading to

1702-416: 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. CRESS-DNA viruses include three kingdoms that infect prokaryotes: Loebvirae , Sangervirae , and Trapavirae . The kingdom Shotokuvirae contains eukaryotic CRESS-DNA viruses and

1748-430: The realm. Adnaviria takes the first part of its name, Adna -, from A-DNA, referring to the A-form genomic DNA of all viruses in the realm. The second part, - viria is the suffix used for virus realms. The sole kingdom in the realm, Zilligvirae , is named after Wolfram Zillig (1925–2005) for his research on hyperthermophilic archaea, with the virus kingdom suffix - virae . The name of the sole phylum, Taleaviricota ,

1794-897: The realm. Notable disease-causing viruses in Varidnaviria include adenoviruses , poxviruses , and the African swine fever virus . Poxviruses have been highly prominent in the history of modern medicine, especially Variola virus , which caused smallpox . Many varidnaviruses are able to become endogenized, and a peculiar example of this are virophages , which confer protection for their hosts against giant viruses during infection. Realm Adnaviria unifies archaeal filamentous viruses with linear A-form double-stranded DNA genomes and characteristic major capsid proteins unrelated to those encoded by other known viruses. The realm currently includes viruses from three families, Lipothrixviridae , Rudiviridae , and Tristromaviridae , all infecting hyperthermophilic archaea. The nucleoprotein helix of adnaviruses

1840-411: The realms generally have no genetic relation to each other, there are some exceptions: In virology, the second highest taxonomy rank established by the ICTV is subrealm, which is the rank below realm. Subrealms of viruses use the suffix - vira , viroid subrealms use the suffix - viroida , and satellites use the suffix - satellitida . The rank below subrealm is kingdom. As of 2019, no taxa are described at

1886-432: The reversibility of many reactions catalyzed by inverting glycosyltransferases served as a paradigm shift in the field and raises questions regarding the designation of sugar nucleotides as 'activated' donors. Sequence-based classification methods have proven to be a powerful way of generating hypotheses for protein function based on sequence alignment to related proteins. The carbohydrate-active enzyme database presents

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1932-408: The stereochemistry of the donor's anomeric bond is retained (α→α) or inverted (α→β) during the transfer. The inverting mechanism is straightforward, requiring a single nucleophilic attack from the accepting atom to invert stereochemistry. The retaining mechanism has been a matter of debate, but there exists strong evidence against a double displacement mechanism (which would cause two inversions about

1978-467: 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 single-stranded DNA (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

2024-472: The three domains of cellular life— Archaea , Bacteria , and Eukarya —which share a common ancestor. Likewise, viruses within each realm are not necessarily descended from a common ancestor since realms group viruses together based on highly conserved traits, not common ancestry, which is used as the basis for the taxonomy of cellular life. As such, each virus realm is considered to represent at least one instance of viruses coming into existence. By realm: While

2070-498: Was difficult to determine deep evolutionary relations between viruses, in the 21st century methods such as metagenomics and cryogenic electron microscopy have enabled such research to occur, which led to the establishment of Riboviria in 2018, three realms in 2019, and two in 2020. The names of realms consist of a descriptive first part and the suffix - viria , which is the suffix used for virus realms. The first part of Duplodnaviria means "double DNA", referring to dsDNA viruses,

2116-437: Was established in 2019 after the relation and origin of CRESS-DNA viruses was resolved, and Varidnaviria was established 2019 based on the shared characteristics of member viruses. Glycosyltransferase Glycosyltransferases ( GTFs , Gtfs ) are enzymes ( EC 2.4 ) that establish natural glycosidic linkages . They catalyze the transfer of saccharide moieties from an activated nucleotide sugar (also known as

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