Misplaced Pages

#409590

73-400: See text Potyvirus is a genus of positive-strand RNA viruses (named after its type species, Potato virus Y (PVY) ) in the family Potyviridae . Plants serve as natural hosts. Like begomoviruses , members of this genus may cause significant losses in agricultural, pastoral, horticultural , and ornamental crops. More than 200 species of aphids spread potyviruses, and most are from

146-438: A genome and as messenger RNA ; it can be directly translated into protein in the host cell by host ribosomes . The first proteins to be expressed after infection serve genome replication functions; they recruit the positive-strand viral genome to viral replication complexes formed in association with intracellular membranes. These complexes contain proteins of both viral and host cell origin, and may be associated with

219-468: A transmembrane domain , 6K1 is thought to contribute to virus-induced vesicle formation. 6K2 (~6 kDa) is a transmembrane protein which rearranges host membranes into virus-induced membrane structures. It interacts with various ER exit site proteins to produce vesicular and tubular extensions which eventually mature into replication vesicles. 6K2 has three main domains: the N-terminal domain which

292-505: A 3-basepair DNA sequence to generate 3-finger, 4-, 5-, or 6-finger arrays that recognize target sites ranging from 9 basepairs to 18 basepairs in length. Another method uses 2-finger modules to generate zinc finger arrays with up to six individual zinc fingers. The Barbas Laboratory of The Scripps Research Institute used phage display to develop and characterize zinc finger domains that recognize most DNA triplet sequences while another group isolated and characterized individual fingers from

365-515: A bacterial two-hybrid system and has been dubbed "OPEN" by its creators. This system combines pre-selected pools of individual zinc fingers that were each selected to bind a given triplet and then utilizes a second round of selection to obtain 3-finger arrays capable of binding a desired 9-bp sequence. This system was developed by the Zinc Finger Consortium as an alternative to commercial sources of engineered zinc finger arrays. It

438-425: A central hollow cylinder from which laminate sheets radiate outward and fold in on themselves in a pattern often described as " pinwheels ". These inclusions are easily seen in transmission electron micrographs of infected tissues and were historically used as a diagnostic criterion for potyvirus infections. CI inclusions are a major component of the potyviral movement complex which is assembled at plasmodesmata . CI

511-435: A double-strand break to a desired genomic locus can be used to introduce frame-shift mutations into the coding sequence of a gene due to the error-prone nature of the non-homologous DNA repair pathway. If a homologous DNA "donor sequence" is also used then the genomic locus can be converted to a defined sequence via the homology directed repair pathway. An ongoing clinical trial is evaluating Zinc finger nucleases that disrupt

584-510: A few. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Initially, the term zinc finger was used solely to describe DNA-binding motif found in Xenopus laevis ; however, it is now used to refer to any number of structures related by their coordination of a zinc ion. In general, zinc fingers coordinate zinc ions with a combination of cysteine and histidine residues. Originally,

657-513: A given DNA target from a large pool of partially randomized zinc finger arrays. This technique is difficult to use on more than a single zinc finger at a time, so a multi-step process that generated a completely optimized 3-finger array by adding and optimizing a single zinc finger at a time was developed. More recent efforts have utilized yeast one-hybrid systems, bacterial one-hybrid and two-hybrid systems, and mammalian cells. A promising new method to select novel 3-finger zinc finger arrays utilizes

730-667: A given gene can be used to alter the transcription of that gene. Fusions between engineered zinc finger arrays and protein domains that cleave or otherwise modify DNA can also be used to target those activities to desired genomic loci. The most common applications for engineered zinc finger arrays include zinc finger transcription factors and zinc finger nucleases , but other applications have also been described. Typical engineered zinc finger arrays have between 3 and 6 individual zinc finger motifs and bind target sites ranging from 9 basepairs to 18 basepairs in length. Arrays with 6 zinc finger motifs are particularly attractive because they bind

803-648: A high level of homology with the picornaviral 3C protease . VPg (~22 kDa) is covalently attched to the 5' end of the viral genomic RNA through uridylation and is thought to act as a primer for viral genome replication similarly to the VPg proteins of picornaviridae . It is a highly disordered protein and its flexibility has been suggested to allow it to interact with many other viral proteins. VPg also interacts with various host proteins including eukaryotic initiation factor 4E (eIF4E), eukaryotic elongation factor 1A (eEF1A), and poly(A)-binding protein (PABP). NIb (~59 kDa)

SECTION 10

#1732791670410

876-466: A loop and a second β-hairpin of varying length and conformation can be present between the N-terminal β-hairpin and the C-terminal α-helix. These fingers are present in a diverse group of proteins that frequently do not share sequence or functional similarity with each other. The best-characterized proteins containing treble-clef zinc fingers are the nuclear hormone receptors . The zinc ribbon fold

949-553: A sister clade in relation to Lenarviricota . The third phylum that contains +ssRNA viruses is Pisuviricota , which has been informally called the "picornavirus supergroup". The phylum contains a large assemblage of eukaryotic viruses known to infect animals, plants, fungi, and protists. The phylum contains three classes, two of which contain only +ssRNA viruses: Pisoniviricetes , which contains nidoviruses , picornaviruses , and sobeliviruses , and Stelpaviricetes , which contains potyviruses and astroviruses . The third class

1022-466: A specific sequence is an area of active research, and zinc finger nucleases and zinc finger transcription factors are two of the most important applications of this to be realized to date. Zinc fingers were first identified in a study of transcription in the African clawed frog , Xenopus laevis in the laboratory of Aaron Klug . A study of the transcription of a particular RNA sequence revealed that

1095-513: A target site that is long enough to have a good chance of being unique in a mammalian genome. Engineered zinc finger arrays are often fused to a DNA cleavage domain (usually the cleavage domain of FokI ) to generate zinc finger nucleases . Such zinc finger-FokI fusions have become useful reagents for manipulating genomes of many higher organisms including Drosophila melanogaster , Caenorhabditis elegans , tobacco , corn , zebrafish , various types of mammalian cells, and rats . Targeting

1168-506: A unique three-dimensional architecture. A particular zinc finger protein's class is determined by its three-dimensional structure, but it can also be recognized based on the primary structure of the protein or the identity of the ligands coordinating the zinc ion. In spite of the large variety of these proteins, however, the vast majority typically function as interaction modules that bind DNA , RNA , proteins, or other small, useful molecules, and variations in structure serve primarily to alter

1241-554: A variety of functions such as binding RNA and mediating protein-protein interactions, but is best known for its role in sequence-specific DNA-binding proteins such as Zif268 (Egr1). In such proteins, individual zinc finger domains typically occur as tandem repeats with two, three, or more fingers comprising the DNA-binding domain of the protein. These tandem arrays can bind in the major groove of DNA and are typically spaced at 3-bp intervals. The α-helix of each domain (often called

1314-733: A variety of host organelles and the sources differ between potyvirus species. Some membrane sources include the ER , chloroplasts , Golgi apparatus , and vacuoles . The exact replication mechanism is not known but it involves a negative sense RNA intermediate and requires both viral and host proteins. Viral proteins detected in replication complexes include HC-Pro, P3, 6K1, 6K2, CI, VPg, NIa-Pro, and NIb. Host factors present in replication vesicles include eIF4A and several heat shock proteins . Like most plant viruses, potyviruses have evolved to move from one plant cell to another through plasmodesmata . However, unlike some well-studied plant viruses, such as

1387-409: Is Duplopiviricetes , whose members are double-stranded RNA viruses that are descended from +ssRNA viruses. Zinc finger Proteins that contain zinc fingers ( zinc finger proteins ) are classified into several different structural families. Unlike many other clearly defined supersecondary structures such as Greek keys or β hairpins , there are a number of types of zinc fingers, each with

1460-588: Is a cysteine protease which cleaves a glycine -glycine dipeptide at its own C-terminus . It also interacts with eukaryotic initiation factor 4 (eIF4). It acts as a viral RNA silencing suppressor through its interactions with host AGO proteins. HC-Pro's activity is regulated by the adjacent P1 protein: before P1 cleaves itself off the P1-HC-Pro intermediate, the P1 terminus reduces HC-Pro's RNA silencing suppression activity. The rate of P1 cleavage therefore regulates

1533-428: Is a serine protease which facilitates its own cleavage from the polyprotein at the P1-HC-Pro junction. P1 consists of a conserved C-terminal protease domain and an N-terminal region which has a high level of variation in sequence and length between potyvirus species but exhibits conserved patterns of intrinsic disorder . P1 is also promotes viral RNA replication, though it is not required for it. HC-Pro (~52 KDa)

SECTION 20

#1732791670410

1606-412: Is a superfamily II RNA-dependent RNA polymerase (RdRp) which polymerises viral RNA during replication. Like NIa, NIb forms inclusions in the host nucleus where it is transported due to its two nuclear localisation sequences . NIb has the three-domain "palm, thumb, and fingers" structure typical of RdRps. 6K1 (~6 kDa) the function is not known, but because it accumulates in replication vesicles and has

1679-502: Is about 1.15 × 10 nucleotide substitutions/site/year. Agriculture was introduced into Australia in the 18th century. This introduction also included plant pathogens. Thirty eight potyvirus species have been isolated in Australia. Eighteen potyviruses have been found only in Australia and are presumed to be endemic there. The remaining twenty appear to have been introduced with agriculture. Historically, potyvirus diagnostics relied on

1752-424: Is also required for viral replication and is present on replication membranes. Its exact contributions to replication are not clear but, as an RNA helicase, CI is likely facilitating replication by dismantling the secondary structures of viral RNA. NIa (~50 kDa) forms crystalline inclusions in the host nucleus. It is cleaved into NIa-Pro and VPg. NIa-Pro (~27 kDa) is a cysteine protease which processes most of

1825-682: Is best suited for most applications. The most straightforward method to generate new zinc finger arrays is to combine smaller zinc finger "modules" of known specificity. The structure of the zinc finger protein Zif268 bound to DNA described by Pavletich and Pabo in their 1991 publication has been key to much of this work and describes the concept of obtaining fingers for each of the 64 possible base pair triplets and then mixing and matching these fingers to design proteins with any desired sequence specificity. The most common modular assembly process involves combining separate zinc fingers that can each recognize

1898-450: Is characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites. The canonical members of this class contain a binuclear zinc cluster in which two zinc ions are bound by six cysteine residues. These zinc fingers can be found in several transcription factors including the yeast Gal4 protein. The zinc finger antiviral protein ( ZAP ) binds to the CpG site. It

1971-473: Is further disrupted by viral proteases degrading components required to initiate translation of cellular mRNA. All positive-strand RNA virus genomes encode RNA-dependent RNA polymerase , a viral protein that synthesizes RNA from an RNA template. Host cell proteins recruited by +ssRNA viruses during replication include RNA-binding proteins , chaperone proteins , and membrane remodeling and lipid synthesis proteins, which collectively participate in exploiting

2044-678: Is not known whether cap-independent translation is an important translation mechanism for potyviruses. Like many other positive strand RNA viruses , potyvirus replication is heavily associated with host membranes. The viral 6K2 protein coordinates the rearrangement of host membranes into various infection-associated structures which, depending on the potyvirus species, can include anything from small round viral vesicles to complex globular structures with many cisternae or lobes. These structures are dotted with viral replication complexes and are often called "replication vesicles", "viroplasm" or "viral factories". Replication vesicle membranes are derived from

2117-595: Is released into host cytoplasm. Potyviral RNA mimicks host mRNA : the 5' VPg protein shares functional similarities with the 5' cap and the 3' end is polyadenylated . VPg and its interactions with eIF4E and eIF4(iso)E allow the virus to utilise host cap-dependent translation machinery for its translation. Similarly to eukaryotic translation, the VPg-eIF4E interaction assembles the eIF4F complex around viral RNA. A number of weak internal ribosome entry sites (IRES) have been identified in many potyvirus species but it

2190-466: Is required for cell-to-cell movement, the central hydrophobic transmembrane alpha helix , and the C terminal domain which is required for viral replication. P3N-PIPO (~25 kDa) is a dedicated movement protein which anchors the movement complex to the plasmodesma . It may also modulate the plasmodesmatal size exclusion limit by interacting with host proteins which sever plasmodesmatal actin filaments and reduce callose deposition. It interacts with both

2263-408: Is used in mammals for antiviral defense. Various protein engineering techniques can be used to alter the DNA-binding specificity of zinc fingers and tandem repeats of such engineered zinc fingers can be used to target desired genomic DNA sequences. Fusing a second protein domain such as a transcriptional activator or repressor to an array of engineered zinc fingers that bind near the promoter of

Potyvirus - Misplaced Pages Continue

2336-680: The Retroviridae (e.g. HIV ), genome damage appears to be avoided during reverse transcription by strand switching, a form of recombination. Recombination occurs in the Coronaviridae (e.g. SARS ). Recombination in RNA viruses appears to be an adaptation for coping with genome damage. Recombination can also occur infrequently between +ssRNA viruses of the same species but of divergent lineages. The resulting recombinant viruses may sometimes cause an outbreak of infection in humans, as in

2409-480: The host cell's ribosomes . Positive-strand RNA viruses encode an RNA-dependent RNA polymerase (RdRp) which is used during replication of the genome to synthesize a negative-sense antigenome that is then used as a template to create a new positive-sense viral genome. Positive-strand RNA viruses are divided between the phyla Kitrinoviricota , Lenarviricota , and Pisuviricota (specifically classes Pisoniviricetes and Stelpavirictes ) all of which are in

2482-480: The Tobacco mosaic virus , potyviruses do not have a single movement protein but instead assemble a movement complex around the plasmodesma. This complex is primarily composed of three viral proteins: CI, CP, P3N-PIPO. Conical CI inclusions are anchored to plasmodesmata by P3N-PIPO during the early stages of potyvirus infection. This allows the inclusion to funnel either viral particles or viral RNA-CP complexes through

2555-414: The "recognition helix") can make sequence-specific contacts to DNA bases; residues from a single recognition helix can contact four or more bases to yield an overlapping pattern of contacts with adjacent zinc fingers. This fold group is defined by two short β-strands connected by a turn (zinc knuckle) followed by a short helix or loop and resembles the classical Cys 2 His 2 motif with a large portion of

2628-552: The CCR5 gene in CD4 human T-cells as a potential treatment for HIV/AIDS . The majority of engineered zinc finger arrays are based on the zinc finger domain of the murine transcription factor Zif268, although some groups have used zinc finger arrays based on the human transcription factor SP1. Zif268 has three individual zinc finger motifs that collectively bind a 9 bp sequence with high affinity. The structure of this protein bound to DNA

2701-482: The Cys 2 His 2 -like (the "classic zinc finger"), treble clef, and zinc ribbon. The following table shows the different structures and their key features: The Cys 2 His 2 -like fold group (C2H2) is by far the best-characterized class of zinc fingers, and is common in mammalian transcription factors. Such domains adopt a simple ββα fold and have the amino acid sequence motif : This class of zinc fingers can have

2774-562: The P3 protein, which is generated into a subset of transcripts by a +2 frameshift caused by a ribosome slippage mechanism at a conserved GA 6 repeat sequence. The resulting protein is called P3N-PIPO. A similar mechanism is thought to produce an alternative reading frame within the P1 cistron, named "pretty interesting sweet potato potyvirus ORF" (PISPO), in a number of sweet potato-infecting potyviruses including sweet potato feathery mottle virus . P1 (~33 kilo daltons (kDa) in molecular weight)

2847-841: The aphid and typically only persist in the aphid for a few minutes. Certain potyviruses have been shown to alter the feeding patterns of their aphid vectors, which may manifest as longer periods of time spent on infected plants, reduced non-probing feeding time, and increased phloem sap ingestion. Seed and pollen transmission has been documented in certain potyvirus species, for instance in PVY and Turnip mosaic virus (TUMV) . Vegetative transmission by infected tubers or grafting material are of particular concern for certain agricultural crops, such as potato and fruit trees, respectively. Transmission can also occur by physical contact with infected plants or with contaminated tools, clothes, or even water. After entry, potyvirus particles are uncoated and genomic RNA

2920-478: The apparent descendants of leviviruses, which infect eukaryotes . The phylum is divided into four classes: Leviviricetes , which contains leviviruses and their relatives, Amabiliviricetes , which contains narnaviruses and their relatives, Howeltoviricetes , which contains mitoviruses and their relatives, and Miaviricetes , which contains botourmiaviruses and their relatives. Based on phylogenetic analysis of RdRp, all other RNA viruses are considered to comprise

2993-405: The binding specificity of a particular protein. Since their original discovery and the elucidation of their structure, these interaction modules have proven ubiquitous in the biological world and may be found in 3% of the genes of the human genome. In addition, zinc fingers have become extremely useful in various therapeutic and research capacities. Engineering zinc fingers to have an affinity for

Potyvirus - Misplaced Pages Continue

3066-461: The binding strength of a small transcription factor (transcription factor IIIA; TFIIIA) was due to the presence of zinc-coordinating finger-like structures. Amino acid sequencing of TFIIIA revealed nine tandem sequences of 30 amino acids, including two invariant pairs of cysteine and histidine residues. Extended x-ray absorption fine structure confirmed the identity of the zinc ligands: two cysteines and two histidines. The DNA-binding loop formed by

3139-458: The canonical pattern of interactions of zinc fingers with DNA. The binding of zinc finger is found to be distinct from many other DNA-binding proteins that bind DNA through the 2-fold symmetry of the double helix, instead zinc fingers are linked linearly in tandem to bind nucleic acid sequences of varying lengths. Zinc fingers often bind to a sequence of DNA known as the GC box . The modular nature of

3212-747: The case of SARS and MERS. Positive-strand RNA viruses are common in plants. In tombusviruses and carmoviruses , RNA recombination occurs frequently during replication. The ability of the RNA-dependent RNA polymerase of these viruses to switch RNA templates suggests a copy choice model of RNA recombination that may be an adaptive mechanism for coping with damage in the viral genome. Other +ssRNA viruses of plants have also been reported to be capable of recombination, such as Brom mosaic bromovirus and Sindbis virus . Positive-strand RNA viruses are found in three phyla: Kitrinoviricota , Lenarviricota , and Pisuviricota , each of which are assigned to

3285-453: The cell's secretory pathway for viral replication. Numerous positive-strand RNA viruses can undergo genetic recombination when at least two viral genomes are present in the same host cell. The capability for recombination among +ssRNA virus pathogens of humans is common. RNA recombination appears to be a major driving force in determining genome architecture and the course of viral evolution among Picornaviridae (e.g. poliovirus). In

3358-595: The cleavage sites of the polyprotein. The only exceptions are the self-cleavages of P1 and HC-Pro. The high degree of cleavage sequence specificity and conservation has made NIa-Pro (often that of Tobacco etch virus ) a valuable tool in biotechnology, especially in applications which require removing affinity tags from recombinant proteins after affinity purification . NIa-Pro has also shown to exhibit sequence-independent DNase activity and to interfere with host DNA methylation suggesting that NIa and/or NIa-Pro are altering in host gene expression . Potyviral NIa-Pro shares

3431-610: The coordination of these ligands by zinc were thought to resemble fingers, hence the name. This was followed soon thereafter by the discovery of the Krüppel factor in Drosophila by the Schuh team in 1986. More recent work in the characterization of proteins in various organisms has revealed the importance of zinc ions in polypeptide stabilization. The crystal structures of zinc finger-DNA complexes solved in 1991 and 1993 revealed

3504-519: The coronaviruses and rhinoviruses that cause the common cold . Positive-strand RNA virus genomes usually contain relatively few genes, usually between three and ten, including an RNA-dependent RNA polymerase. Coronaviruses have the largest known RNA genomes, between 27 and 32 kilobases in length, and likely possess replication proofreading mechanisms in the form of an exoribonuclease within nonstructural protein nsp14. Positive-strand RNA viruses have genetic material that can function both as

3577-557: The detection of various proteinaceous inclusions in infected plant cells. These may appear as crystals in either the cytoplasm or in the nucleus, as amorphous X-bodies, membranous bodies, viroplasms or pinwheels. The inclusions may or may not (depending on the species) contain virions. These inclusions can be seen by light microscopy in leaf strips of infected plant tissue stained with Orange-Green (protein stain) but not Azure A (nucleic acid stain). Modern detection methods rely primarily on reverse transcription PCR . Potyvirus contains

3650-413: The finger-like folds . They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein, and/or lipid substrates . Their binding properties depend on the amino acid sequence of the finger domains and on the linker between fingers, as well as on the higher-order structures and

3723-557: The following species: A further four viruses were previously classified as species in this genus but were abolished due to lack of genetic sequence information: Potyviruses were further divided into the PVY, SCMV, BYMV, BCMV species groups in 1992. Gibbs and Ohshima 2010 produced a more extensive molecular phylogeny with the same four, but also several new groups: the BtMV, ChVMV, DaMV, OYDV, PRSV, TEV, and TuMV. Contains 16 species including

SECTION 50

#1732791670410

3796-616: The helix and β-hairpin truncated. The retroviral nucleocapsid (NC) protein from HIV and other related retroviruses are examples of proteins possessing these motifs. The gag-knuckle zinc finger in the HIV NC protein is the target of a class of drugs known as zinc finger inhibitors . The treble-clef motif consists of a β-hairpin at the N-terminus and an α-helix at the C-terminus that each contribute two ligands for zinc binding, although

3869-460: The human genome. A potential drawback with modular assembly in general is that specificities of individual zinc finger can overlap and can depend on the context of the surrounding zinc fingers and DNA. A recent study demonstrated that a high proportion of 3-finger zinc finger arrays generated by modular assembly fail to bind their intended target with sufficient affinity in a bacterial two-hybrid assay and fail to function as zinc finger nucleases , but

3942-465: The interactions between replication vesicles and movement complex proteins which may allow replication vesicles to be recruited to the movement complex for efficient intercellular movement. P3 also interacts with large subunit of the ribulose-1,5-bisphosphate carboxylase/oxygenase . CI (~71 kDa) is an RNA helicase with ATPase activity. Its most unusual property is its ability to form large and highly symmetrical conical and cylindrical inclusions with

4015-604: The kingdom Orthornavirae and realm Riboviria . They are monophyletic and descended from a common RNA virus ancestor. In the Baltimore classification system, +ssRNA viruses belong to Group IV. Positive-sense RNA viruses include pathogens such as the Hepatitis C virus , West Nile virus , dengue virus , and the MERS , SARS , and SARS-CoV-2 coronaviruses , as well as less clinically serious pathogens such as

4088-423: The kingdom Orthornavirae in the realm Riboviria . In the Baltimore classification system, which groups viruses together based on their manner of mRNA synthesis, +ssRNA viruses are group IV. The first +ssRNA phylum is Kitrinoviricota . The phylum contains what have been referred to as the " alphavirus supergroup" and " flavivirus supergroup" along with various other short-genome viruses. Four classes in

4161-468: The large and small subunits of the ribulose-1,5-bisphosphate carboxylase/oxygenase. CP (~30 - 35 kDa) is the capsid protein. It has two terminal domains which are disordered and exposed at the surface of the virion. The central core domain contains an RNA-binding pocket which binds to viral RNA. The structure of the capsid protein is highly conserved in potyviruses, though there is a relatively high degree of sequence variability. In addition to encapsidating

4234-462: The level of RNA interference suppression during infection. HC-Pro is also involved in aphid transmission. Though the exact mechanism is unknown, HC-Pro has been proposed to attach to host aphid mouth parts through its N-terminal zinc finger -like domain and anchor virions through its interactions with the capsid protein. P3 (~41 kDa) is a membrane protein which is required for viral replication and accumulates in viral replication vesicles. It mediates

4307-455: The membranes of a variety of organelles —often the rough endoplasmic reticulum , but also including membranes derived from mitochondria , vacuoles , the Golgi apparatus , chloroplasts , peroxisomes , plasma membranes , autophagosomal membranes , and novel cytoplasmic compartments. The replication of the positive-sense RNA genome proceeds through double-stranded RNA intermediates, and

4380-483: The nucleocapsid is helical with a pitch of 3.4-3.5 nm. The genome is a linear, positive-sense , single-stranded RNA ranging in size from 9,000 to 12,000 nucleotide bases . Most potyviruses have non-segmented genomes, though a number of species are bipartite. The typical base compositions of some of the most common, non-recombinant strains of the type species, PVY, range between ~23.4-23.8 % G; ~31-31.6 % A; ~18.2-18.8 % C; and ~26.5-26.8 % U. In

4453-425: The number and order of these residues was used to classify different types of zinc fingers ( e.g., Cys 2 His 2 , Cys 4 , and Cys 6 ). More recently, a more systematic method has been used to classify zinc finger proteins instead. This method classifies zinc finger proteins into "fold groups" based on the overall shape of the protein backbone in the folded domain. The most common "fold groups" of zinc fingers are

SECTION 60

#1732791670410

4526-694: The number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. Znf motifs occur in several unrelated protein superfamilies , varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g., some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organization, epithelial development, cell adhesion , protein folding, chromatin remodeling, and zinc sensing, to name but

4599-451: The phylum are recognized: Alsuviricetes , the alphavirus supergroup, which contains a large number of plant viruses and arthropod viruses; Flasuviricetes , which contains flaviviruses, Magsaviricetes , which contains nodaviruses and sinhaliviruses ; and Tolucaviricetes , which primarily contains plant viruses. Lenarviricota is the second +ssRNA phylum. It contains the class Leviviricetes , which infect prokaryotes , and

4672-497: The plasmodesma. Replication vesicles are also recruited to the movement complex, suggesting that replication and movement are coupled. Replication vesicles are recruited by P3N-PIPO, which interacts with both CI and P3 through the shared P3N-domain. P3's interaction with 6K2 allows replication vesicles to be tethered to the movement complex. Potyviruses evolved between 6,600 and 7,250 years ago. They appear to have evolved in southwest Eurasia or north Africa . The estimated mutation rate

4745-528: The purpose of replication in these membranous invaginations may be the avoidance of cellular response to the presence of dsRNA. In many cases subgenomic RNAs are also created during replication. After infection, the entirety of the host cell's translation machinery may be diverted to the production of viral proteins as a result of the very high affinity for ribosomes by the viral genome's internal ribosome entry site (IRES) elements; in some viruses, such as poliovirus and rhinoviruses , normal protein synthesis

4818-726: The species with a monopartite genome, a genome-linked VPg protein is covalently bound to the 5' end and the 3' end is polyadenylated. The genome encodes a single open reading frame (ORF) expressed as a 350 kDa polyprotein precursor. This polyprotein is processed into ten smaller proteins: protein 1 protease (P1-Pro), helper component protease (HC-Pro), protein 3 (P3), cylindrical inclusion (CI), viral protein genome-linked (Vpg), nuclear inclusion A (NIa), nuclear inclusion B (NIb), capsid protein (CP) and two small putative proteins known as 6K1 and 6K2. The P3 cistron also contains an overlapping reading frame called "Pretty interesting Potyviridae ORF " (PIPO). PIPO codes for an alternative C-terminus to

4891-419: The subfamily Aphidinae (genera Macrosiphum and Myzus ). The genus contains 190 species and potyviruses account for about thirty percent of all currently known plant viruses . The virion is non-enveloped with a flexuous and filamentous nucleocapsid , 680 to 900 nanometers (nm) long and is 11–20 nm in diameter. The nucleocapsid contains around 2000 copies of the capsid protein. The symmetry of

4964-689: The success rate was somewhat higher when sites of the form GNNGNNGNN were targeted. A subsequent study used modular assembly to generate zinc finger nucleases with both 3-finger arrays and 4-finger arrays and observed a much higher success rate with 4-finger arrays. A variant of modular assembly that takes the context of neighboring fingers into account has also been reported and this method tends to yield proteins with improved performance relative to standard modular assembly. Numerous selection methods have been used to generate zinc finger arrays capable of targeting desired sequences. Initial selection efforts utilized phage display to select proteins that bound

5037-486: The type species of the genus (potato virus Y). The primary hosts are: Nine Solanaceae , three Amaranthus , three Asteraceae , one Lilium , and one Amaryllis . Positive-strand RNA virus Positive-strand RNA viruses ( +ssRNA viruses ) are a group of related viruses that have positive-sense , single-stranded genomes made of ribonucleic acid . The positive-sense genome can act as messenger RNA (mRNA) and can be directly translated into viral proteins by

5110-519: The virion, CP core domain is required for intercellular movement and contributes to seed transmission. Certain atypical potyviruses code for additional proteins or protein domains, such as P1-PISPO, Alkylation B (AlkB) , and inosine triphosphate pyrophosphatase (known as ITPase or HAM1). Such anomalies are often situated in the hypervariable P1-HC-Pro region. Most potyviruses are transmitted by aphids as they probe plant tissues with their stylet during feeding. They do not circulate or multiply within

5183-524: The zinc finger motif allows for a large number of combinations of DNA and RNA sequences to be bound with high degree of affinity and specificity, and is therefore ideally suited for engineering protein that can be targeted to and bind specific DNA sequences. In 1994, it was shown that an artificially-constructed three-finger protein can block the expression of an oncogene in a mouse cell line. Zinc fingers fused to various other effector domains, some with therapeutic significance, have since been constructed. Such

5256-740: Was its importance that "the zinc-finger motif" was cited in the Scientific Background to the 2024 Nobel Prize in Chemistry (awarded to David Baker , Demis Hassabis , and John M. Jumper for computational protein design and protein structure prediction). Zinc finger (Znf) domains are relatively small protein motifs that contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not, instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise

5329-399: Was solved in 1991 and stimulated a great deal of research into engineered zinc finger arrays. In 1994 and 1995, a number of groups used phage display to alter the specificity of a single zinc finger of Zif268. There are two main methods currently used to generate engineered zinc finger arrays, modular assembly, and a bacterial selection system, and there is some debate about which method

#409590