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Subgenomic mRNA
Subgenomic mRNAs containing the origin of assembly are encapsidated into shorter virions that are not required for infectivity.
From: Encyclopedia of Virology (Second Edition), 1999
Related terms:
RNA-dependent RNA Polymerase
Cytoplasm
Virus Genome
Open Reading Frame
RNA Synthesis
Virion
Arterivirus
Coronavirinae
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SPUMAVIRUSES (RETROVIRIDAE)
Mel Campbell, ... Paul A. Luciw, in Encyclopedia of Virology (Second Edition), 1999
Translation
A subgenomic mRNA encodes the Prt-Pol precursor which lacks Gag determinants. No Gag-Pol precursor can be detected in foamy virus-infected cells or virions. The Env polyprotein precursor is translated from a subgenomic spliced mRNA. The subgenomic mRNA for Env is presumed to be translated on membrane-bound cytoplasmic polysomes, and other viral mRNA species may be translated on free polysomes in the cytoplasm. Proteins encoded by bel-2 and bel-3 have been identified in infected cells. An abundant protein containing N-terminal sequences from the bel-1 gene and C-terminal sequences from the bel-2 gene has been detected in infected cells; however, the function of this fusion protein, designated Bet, is not known.
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Togaviruses: Molecular Biology
K.D. Ryman, ... S.C. Weaver, in Encyclopedia of Virology (Third Edition), 2008
Structural Protein Maturation, Genome Packaging, and Egress of Virions
The subgenomic mRNAs of alphaviruses and of Rubella virus are translated as polyproteins; however, processing of the polyprotein differs between the two. With alphaviruses, the capsid protein is cleaved autoproteolytically from the E2 precursor (known as PE2 or P62) in the cytoplasm and the remaining polyprotein is translocated into the ER lumen, where N-linked oligosaccharide addition occurs. The 6K hydrophobic protein, which is primarily located in the ER membrane, is then cleaved from the polyprotein by the host signalase. With Rubella virus, the capsid-E2 and E2–E1 cleavages are all completed by signalase. Furthermore, Rubella virus lacks the 6K protein and mature E2 is produced in the ER. Alphavirus PE2 and E1 proteins form heterodimers in the ER that are anchored by their transmembrane domains and involve intra- and intermolecular disulfide linkages and associations with host chaperone proteins such as Bip and calnexin/calreticulin. The PE2/E1 heterodimers are routed to the cytoplasmic membrane and PE2 is cleaved into mature E2 by a host furin-like protease as a late event, in a structure between the trans Golgi network and cell surface. The cleaved E3 fragment is lost from some (e.g., SINV), but not all (e.g., SFV) virus particles. PE2-containing virions appear to bud normally from vertebrate cells, but are often defective in conformational rearrangements associated with cell fusion, supporting the hypothesis that the presence of PE2 stabilizes the glycoprotein heterodimer during low pH exposure in the secretory pathway.
Budding of particles occurs through an interaction between C and the cytoplasmic tail of E2; however, it is unclear at which point in the secretory pathway this interaction occurs and whether the interaction is between C monomers, oligomers, or RNA-containing preformed nucleocapsids. With alphaviruses, RNA packaging is directed by an RNA secondary structure in either the nsP1 or nsP2 genes, depending upon the virus, leading to selective packaging of the genome over the subgenome, which is in molar excess. In the accepted model, final budding occurs at the cytoplasmic membrane at sites enriched in E2/E1 heterodimers and is driven by E2 tail-C interactions that force an extrusion of the host lipid bilayer, envelopment of the particle, and release.
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Nidovirales
In Virus Taxonomy, 2012
Synthesis of genomic and subgenomic rnas
Genome replication and sg mRNA synthesis ("transcription") proceed through minus-strand intermediates. The genome serves as a template for the synthesis of full-length minus-strand RNA, from which in turn new genome copies are produced, but it is also believed to be the template for the synthesis of sg minus-strand RNA species (vide infra). The synthesis of viral RNAs is highly asymmetrical as plus-strand RNAs are produced in fast excess.
A hallmark of nidovirus transcription is the production of a 3′-coterminal nested set of sg mRNAs. The sg mRNAs of corona-, arteri- and bafiniviruses are chimeric, that is, comprised of sequences that are non-contiguous in the viral genome. Each carries a short 5′ leader sequence of 55–92, 170–210 nt, and 42 nucleotides, respectively, which is identical to the 5′ end of the viral genome. It was established early on that leader and "body" sequences are not joined through splicing, but via a process of discontinuous RNA synthesis. A key observation was the presence of mirror-copy nested sets of sg minus-strand RNAs in corona- and arterivirus-infected cells. Combined experimental evidence from biochemical and reverse genetics analyses indicates that these sg minus-strand RNAs are in fact the templates for sg mRNA synthesis. Replicative intermediates (RI)/replicative forms with sizes corresponding to the different sg mRNAs were shown to be actively involved in transcription. According to the prevailing 3′-discontinuous extension model, the discontinuous step occurs during the production of sg minus-strand RNAs and entails attenuation of RNA synthesis at the TRSs, followed by a similarity-assisted copy choice RNA recombination event. In corona-, arteri- and bafiniviruses, a TRS is present immediately downstream of the genomic leader sequence. It is believed that, during minus-strand RNA synthesis, the replicase complex upon encounter of an internal TRS dissociates from the template and is transferred to the 5′ end of the genome, guided by sequence complementarity between the anti-TRS on the nascent strand and the genomic TRS. Reinitiation and completion of RNA synthesis would then result in a chimeric minus-strand that in turn would serve as a template for uninterrupted (continuous) synthesis of 5′ leader-containing sg mRNAs.
Discontinuous sg RNA synthesis is not a trait of all nidoviruses. Ronivirus sg mRNAs lack a common 5′ leader and thus apparently arise from non-discontinuous RNA synthesis. Toroviruses employ a mixed transcription strategy; of the four sg RNAs, only RNA 2 carries a 15–18 nt 5′ leader derived from the 5′ end of the genome, whereas the others do not. It is likely that sg mRNAs are transcribed from sg minus-strand templates also in toro- and in roniviruses. Here, the conserved sequence elements (TPs) preceding the 3′-proximal genes might serve dual roles as signals for premature termination of minus-strand synthesis and as promoters for plus-strand production. The torovirus S gene, expressed from mRNA 2, lacks a TP. Apparently, transcription-competent minus-strand sg RNAs are produced by inclusion of a complementary copy of the 5′-terminal genomic TP via a similarity-assisted RNA recombination process analogous to that seen in corona- and arteriviruses.
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Coronaviruses
K. Nakagawa, ... S. Makino, in Advances in Virus Research, 2016
2.3 Changes in the Poly(A) Tail Length During CoV Replication
CoV genomic and subgenomic mRNAs carry a poly(A) tail at their 3′ ends. Hofmann and Brian postulated that viral RNA-dependent RNA polymerase or a cellular cytoplasmic poly(A) polymerase synthesizes the poly(A) tail of CoV mRNAs (Hofmann and Brian, 1991). Wu et al. reported that the length of the poly(A) tail of bovine CoV (BCoV) mRNAs in infected human rectal tumor-18 cells varies at various times postinfection (p.i.), ranging from ~ 45 nt immediately after virus entry to ~ 65 nt at 6–9 h p.i. and ~ 30 nt at 120–144 h p.i. (Wu et al., 2013). Differences in poly(A) length of viral mRNAs at different times p.i. was also observed in several other BCoV-infected cell lines and cells infected with different strains of infectious bronchitis virus (IBV) (Shien et al., 2014), indicating that changes in the poly(A) length during virus replication may be a common feature of CoVs. Factor and mechanisms involved in this process remain to be studied. Because the length of the poly(A) tail contributes to the efficiency of translation and replication of CoV defective interfering RNAs (Spagnolo and Hogue, 2000; Wu et al., 2013), the regulated changes in the length of the CoV poly(A) tail may affect efficiencies of viral translation and replication over the course of infection.
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HIV/AIDS
S. Kaushik, J.A. Levy, in Encyclopedia of Microbiology (Third Edition), 2009
Regulatory and Accessory Proteins
Splicing events resulting in many subgenomic mRNAs are responsible for the synthesis of other viral regulatory and accessory proteins. One of the regulatory proteins essential for HIV replication is Tat, a transcriptional transactivator encoded by two exons. Tat binds to a short stem–loop structure known as the transactivation response element, which is formed in the 3′ portion of the viral LTR. This attachment stabilizes the nascent mRNA and promotes the elongation phase of HIV-1 transcription, so that full-length transcripts can be produced. The second regulatory protein, Rev (regulator of viral protein expression), is a sequence-specific RNA-binding protein that binds to a 240-base region of a complex RNA secondary structure, called the Rev response element (RRE) located in the viral envelope mRNA. This interaction permits unspliced mRNA to enter the cytoplasm from the nucleus and gives rise to the viral proteins from unspliced and singly spliced mRNAs that are needed for progeny production.
HIV contains four additional genes, nef, vif, vpr, and vpu (vpx in HIV-2), encoding the so-called accessory proteins. Nef (negative factor) protein has been shown to have multiple activities, including downregulation of the cell surface expression of CD4, perturbation of T cell activation, and stimulation of HIV infectivity. Viruses with Nef deleted do not replicate well in PBMCs or in vivo. The other accessory gene products, Vpr, Vpu, Vpx and Vif, are involved in virion assembly, cell cycling and budding, and infectivity during the production of infectious viruses. The importance of Vif lies in its countering the intracellular resistance factor APOBEC3G (see 'Intracellular factors').
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Gene Therapy
JAMES H. STRAUSS, ELLEN G. STRAUSS, in Viruses and Human Disease (Second Edition), 2008
Polioviruses
Plus-strand viruses that do not produce subgenomic mRNAs, such as the picornaviruses and flaviviruses, present different problems for development as vectors. The translated product from the gene of interest must either be incorporated into the polyprotein produced by the virus and provisions made for its excision, or tricks must be used to express the gene of interest independently. Two approaches with poliovirus will be described as examples of how such viruses might be used as vectors.
Poliovirus replicons have been constructed by deleting the region encoding the structural proteins and replacing this sequence with that for a foreign gene. The foreign gene must be in phase with the remainder of the poliovirus polyprotein, and the cleavage site recognized by the viral 2A protease is used to excise the foreign protein from the polyprotein. Because the poliovirus replicon lacks a full complement of the structural genes (it is a suicide vector), packaging to produce particles requires infection of a cell that expresses the polioviral structural proteins by some mechanism. A construct that uses this approach to express the cytokine tumor necrosis factor alpha (TNF-α) is illustrated in Fig. 11.5. A poliovirus "infectious clone" in which a DNA copy of the viral genome is positioned downstream of a promoter for T7 RNA polymerase is modified by replacing the genes for VP3 and VP1 with the gene for TNF-α. Recognition sites for the poliovirus 2A protease are positioned on both sides of the TNF-α gene. The TNF-α protein is produced as part of the poliovirus polyprotein, and cleaved from the polyprotein by the 2A protease. Packaged replicons were used to infect transgenic mice that expressed the polio receptor (Chapter 1). One of the interests of this system is that poliovirus exhibits an extraordinary tropism for motor neurons in the central nervous system (CNS) (Chapter 3). The packaged replicons, on introduction into the CNS, infected only motor neurons, and therefore the foreign gene was expressed only in motor neurons. Such replicons may be useful to treat CNS diseases in which motor neurons are affected.

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FIGURE 11.5. Generation of poliovirus replicons for expression of foreign genes in motor neurons. Based on an earlier construct to express interleukin-2 via a poliovirus replicon, the gene for wild-type murine tumor necrosis factor alpha (TNF-α) was positioned between the VP0 and 2A proteins of poliovirus, replacing VP3 and VP1. It was flanked on either side by sites for cleavage by the poliovirus 2A protease. These constructs were injected into transgenic mice expressing the poliovirus receptor, and expression of murine TNF-α was monitored.
Adapted from Bledsoe et al. (2000).Copyright © 2000
A second approach to the use of poliovirus replicons is to use a second internal ribosome entry site (IRES) (Chapter 1) to initiate the synthesis of the nonstructural proteins. If the foreign gene replaces the structural genes, it will be translated from the 5′ end of the genome. If the poliovirus nonstructural genes are placed downstream of a second IRES, internal initiation at this IRES results in production of a polyprotein for the nonstructural proteins. This approach is similar to the approach shown in Fig. 3.3, where the structural proteins are replaced by a gene of interest.
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Plus-Strand RNA Viruses
JAMES H. STRAUSS, ELLEN G. STRAUSS, in Viruses and Human Disease (Second Edition), 2008
Production of Subgenomic RNAs
The members of the Nidovirales produce a nested set of subgenomic mRNAs (Fig. 3.38), which are capped and polyadenylated. The number produced depends on the virus but is 5 to 8 for most. Each subgenomic RNA is a messenger that is translated into one to three proteins from the 5′ ORF(s) in the mRNA. The five subgenomic mRNAs of IBV and the proteins translated from them are illustrated in Fig. 3.38A. Four of the subgenomic mRNAs are translated into the structural proteins in the virion, S, E, M, and N, found in that order in the genomes of all coronaviruses. Four small accessory proteins of unknown function are also produced, two from the E mRNA and two from RNA 5. Coronaviruses encode variable numbers of such accessory proteins which are not conserved as to sequence or to number among the various members of the family and whose function in unknown. It is also not known how multiple proteins are translated from a single mRNAs in the case of the coronaviruses.
Two mechanisms have been proposed for the production of these subgenomic RNAs. The first mechanism proposed was primer-directed synthesis from the (−)RNA template (i.e., from the antigenome produced from the genomic RNA). In this model, a primer of about 60 nucleotides is transcribed from the 3′ end of the template, which is therefore identical to the 5′ end of the genomic RNA. The primer is proposed to dissociate from the template and to be used by the viral RNA synthetase to reinitiate synthesis at any of the several sub-genomic promoters in the (−)RNA template. Evidence for this model includes the fact that each subgenomic RNA has at its 5′ end the same 60 nucleotides that are present at the 5′ end of the genomic RNA, and that there is a short sequence element present at the beginning of each gene that could act as an acceptor for the primer (this sequence, e.g., is ACGAAC in the SARS CoV). A recent model proposes that the bulk of the subgenomic mRNAs are produced by independent replication of the subgenomic RNAs as replicons. Such replication is thought to be possible because the mRNAs contain both the 5′ and 3′ sequences present in the genomic RNA, and therefore possess the promoters required for replication. Evidence for this model includes the fact that both plus-sense and minus-sense subgenomic RNAs are present in infected cells. The model favored is that the subgenomic RNAs are first produced during synthesis of minus-strand RNA from the genomic RNA. In this model, synthesis initiates at the 3′ end of the genome and then jumps to the 5′ leader at one of the junctions between the genes. Once produced, the subgenomic RNAs begin independent replication.
Coronaviruses undergo high-frequency recombination in which up to 10% of the progeny may be recombinant. It is proposed that the mechanism for generation of the subgenomic RNAs, which requires the polymerase to stop at defined sites and then reinitiate synthesis at defined promoters, may allow the formation of perfect recombinants at high frequency.
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Introduction to Retroviruses
Stephen P. Goff, in AIDS and Other Manifestations of HIV Infection (Fourth Edition), 2004
Env Gene Expression
In all retroviruses the env gene is expressed from a distinct subgenomic mRNA. The env message is a singly spliced mRNA, in which a 5′ leader is joined to the coding region of env. Thus, the bulk of the gag and pol genes are removed as an intron from the mRNA. The resulting message is exported to the cytoplasm and translated from a conventional AUG initiator codon. In the alpharetroviruses, the AUG is actually the same one used for Gag translation; it lies in the leader exon and the splicing brings this AUG and the first six codons into frame with the env coding region. The first translated amino acids constitute a hydrophobic signal peptide, and direct the nascent protein to the rough endoplasmic reticulum. The leader is removed by a cellular protease (the signal protease) in the ER, and the protein is heavily glycosylated by transfer of oligosaccharide from a dolichol carrier to asparagine residues on Env. These residues lie in the conventional Asn-X-Ser/Thr motifs recognized by the modification enzymes. Near the end of the cotranslational insertion of Env into the ER, a highly hydrophobic sequence acts as a stop transfer signal to anchor the protein in the membrane. The remaining C-terminal portion of the protein stays on the cytoplasmic side of the membrane.
Before the Env proteins are transported to the cell surface, they are folded and oligomerized in the ER. The formation of oligomers is required for stable expression of the protein, and is sensitive to overall conformation; many mutants of Env show defects in oligomerization (247). There is considerable controversy about the oligomeric state of the Env protein in different viruses, and at different times during their transport (248–252). The most studied envelope proteins (ASLV and HIV-1) may pass through dimeric or tetrameric intermediates, but the nature of these intermediates is not clear. Although some laboratories disagree (e.g. (253,250,254,255)), ultimately these envelopes probably form trimers in the mature virus (248,256). The folding of the protein is presumably catalyzed by chaperone proteins in the ER; and the formation of disulfide bonds between various pairs of cysteine residues is similarly catalyzed by disulfide interchange enzymes.
The Env protein is then exported to the Golgi, and cleaved by furin proteases to form the separate SU and TM subunits. This cleavage is essential for the normal function of the Env protein. The cleavage occurs at a dibasic pair of amino acids (257), and produces a hydrophobic Nterminus for the TM protein that is required to mediate fusion of the viral and host membranes during virus entry. In the Golgi the sugar residues are modified by the sequential removal of mannose residues and addition of N-acetyl glucosamine and other sugars to many of the oligosaccharide. O-linked glycosylation and sulfation of Env glycoproteins have also been documented (258,259). The pathway by which Env is transported to the cell surface is not fully understood, but presumably host vesicular transport systems are utilized. There is evidence that clathrin adaptor complexes interact with the cytoplasmic tail of Env, and direct its movement to the plasma membrane (260). The protein typically becomes a prominent cell surface protein on the infected cell.
In polarized epithelial cells, Env proteins are often restricted to the basolateral surface of the cell (261). This localization is mediated by a tyrosine-based motif, Yxxϕ, present in the cytoplasmic tail of Env (262,263) (x, any amino acid; ϕ, hydrophobic residue). Remarkably, this targetting of Env can redirect the budding of Gag proteins to this surface.
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Tombusvirus-Like Viruses (Tombusviridae)
K. Andrew White, in Reference Module in Life Sciences, 2020
Gene Expression
Gene expression in these viruses involves cap-independent translation, ribosome readthrough, sg mRNA transcription, and leaky scanning. Intriguingly, for function, all but the latter activity require RNA-RNA interactions that span large distances within the viral genomes (Fig. 5(A)). All tombusvirid RNA genomes lack a 5′-cap and a 3′-poly(A) tail. Instead, they contain one of several types of 3′-cap independent translational enhancer (3′-CITE) in their 3′-untranslated regions (3′-UTRs). 3′-CITEs in the tombusvirus-like group are higher-order RNA structures that bind to translation initiation factor 4F (eIF4F). These 3′-CITEs, while bound to eIF4F, also interact with the 5′-UTRs of their genomes, via a long-range RNA-RNA base pairing interactions (Fig. 5(A)). This positions the bound eIF4F near the 5′-end of the genomes, allowing for 43S subunit recruitment that mediates translation of the auxiliary replication proteins, p33 in the case of TBSV (and the p92 RdRp via readthrough). Though closely related, the three genera contain different types of 3′-CITEs; tombusviruses have Y-shaped versions (except for, Cucumber Bulgarian latent virus, CBLV, which has an I-shaped type), aureusviruses contain either a PTE or I-shaped class, while zeaviruses contain only I-shaped versions. Accordingly, modularity in these viral genomes also exists with respect to translational regulatory RNA elements.
Viral RdRps, such as p92 in TBSV, are expressed by translational readthrough of the stop codon for the auxiliary replication protein. Programmed ribosome readthrough occurs when RNA elements in a message promote the use of near-cognate tRNAs for decoding of a termination codon. In tombusviruses, this process requires an extended stem-loop RNA structure, termed RTSL, positioned just 3′ to the stop codon. However, in order for readthrough to occur, a sequence in RTSL (termed PRTE) must base pair, via a long-range RNA-RNA interaction, with a segment in the 3′-UTR of the genome (DRTE) (Fig. 5(A)). This interaction shuts down minus-strand RNA synthesis during readthrough, thereby preventing a conflict between these processes that occur in opposite directions on the viral genome. Similar local and long-distance RNA structural requirements for readthrough production of RdRp are also predicted for aureusviruses and zeaviruses.
Within the context of tombusvirus-like genomes, the three ORFs encoded in their latter halves are translationally silent. Consequently, expression of these gene products requires the transcription of viral sg mRNAs. During infections, two sg mRNAs are synthesized that encode at their 5′-ends either the capsid protein ORF or the two overlapping ORFs. The capsid protein is translated from the larger sg mRNA1, while both the movement and silencing suppressor are translated from sg mRNA2 (Fig. 5(B)). The latter protein is translated when 43S subunits scan past the more 5′-proximally positioned movement protein start codon and initiate at the downstream suppressor protein start codon, a mechanism referred to as leaky scanning.
Transcription of sg mRNAs involves premature termination of the RdRp while synthesizing complementary genomic minus-strands. RdRp termination occurs when the viral polymerase encounters certain higher-order RNA structures in a genome, called attenuation structures. This results in truncated minus-strands that include transcription initiation sites, for either sg mRNA1 or 2, at their 3′-ends. These sg mRNA-sized minus-strands are then used as templates to transcribe the two different size classes of sg mRNAs. Interestingly, in tombusviruses and zeaviruses, the attenuation RNA structures for both sg mRNA1 and 2 are formed by long-range, base pairing, RNA-RNA interactions (AS1-RS1 and AS2-RS2, respectively) (Fig. 5(A)). These genome-level interactions may provide an RNA-based mechanism to coordinate transcription with other viral processes. Aureusviruses have comparable long-distance AS2-RS2 interactions for sg mRNA2 production, but, for sg mRNA1, the attenuation structure is formed by a locally-folded section of RNA. Although variations in attenuation structures exist, the sg mRNAs generated are structurally similar in that all are 3′-coterminal with their cognate genomes. This feature ensures that these smaller viral messages contain 3′-CITEs, which enhance their translation via cognate 5′UTR-3′CITE interactions.
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TENUIVIRUSES
Bryce W. Falk, in Encyclopedia of Virology (Second Edition), 1999
Gene Expression Strategies
The tenuivirus full-length genomic RNAs are not mRNAs. During tenuivirus infection and replication, specific subgenomic mRNAs are generated for the ambisense genomic RNAs (RNAs 2, 3 and 4; see Fig. 5), and for MSpV, with the exception of that for p4, subgenomic mRNAs have been identified both in MSpV-infected plants and planthoppers. As tenuivirus genomic RNAs 1 and 5 are monocistronic, it is likely that mRNAs for pc1 and pc5 are essentially full-length, but probably are modified from those found in RNPs.
The subgenomic mRNAs representing the RNA 2, RNA 3 and RNA 4 open reading frames (ORFs) have been detected in MSpV-infected tissues, but not in purified RNPs. The sizes of the RNA 2, RNA 3 and RNA 4 subgenomic mRNAs are c. 700 and 2600 nt for p2 and pc2; 650 and 1350 nt for p3 and pc3; and c. 950 and 1000 nt for p4 and pc4, respectively. In agreement with the polarities of the ORFs contained in each of the ambisense genomic RNAs, the subgenomic mRNAs for a given RNA segment are of opposite polarity to each other, and it is likely that subgenomic mRNAs for a given genomic RNA are not overlapping. The opposing ORFs on a specific genomic RNA are separated by relatively large A-U rich intergenic regions (>350 nt). Whether or not these intergenic regions play a role in mRNA transcription termination is not yet known.
The subgenomic mRNAs correspond in nucleotide sequence with the 5′ regions of the genomic RNA segments; however, the 5′ terminal nucleotide sequences for a given genomic RNA (i.e. vRNA 4) and the corresponding mRNA (i.e. that for the p4 ORF) are not identical. The 5′ termini for several tenuivirus mRNAs have been shown to contain short leader sequences of heterogeneous nucleotide composition, and these are immediately 5′ of the viral RNA sequence. Furthermore, and in contrast to the tenuivirus genomic RNAs, the mRNAs have a 5′ cap. It is believed that these capped leader sequences are generally of host mRNA origin and originate by 'cap snatching'.
Cap snatching is a feature which was first described for influenza virus, and which was subsequently shown to occur for other vertebrate-infecting viruses such as those in the families Orthomyxoviridae, Arenaviridae and Bunyaviridae. During mRNA transcription, host mRNAs are recruited and a virus-encoded cap-specific endonuclease cleaves the host mRNA several nucleotides downstream of the 5′ cap. The resulting 5′-capped sequence is then used as a primer for mRNA synthesis. A few of the 3′ nucleotides base pair with the mRNA template (the 3′ end of the full-length RNAs) and the short, capped ribonucleotide serves as a primer for transcription. Thus, the mRNA gains the 5′ cap and short leader sequence of the donor mRNA. The specificity of donor RNAs that can serve as mRNA primers is not yet known, but generally the capped leader sequences are short, only 10–16 nt.
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Fusion Protein
A fusion protein (bRXC) composed by iron–sulfur protein (Pdx) and flavoprotein Pdx reductase (Pdr) with P450cam was prepared through the assembly of linkers attached to each individual component using transglutaminase.
From: Comprehensive Chirality, 2012
Related terms:
Neoplasm
Antibody
Peptide
Protein
Mutation
Amino Terminal Sequence
Carboxy Terminal Sequence
Ligand
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Fusion Protein
P. Riggs, in Brenner's Encyclopedia of Genetics (Second Edition), 2013
Introduction
A fusion protein is a protein consisting of at least two domains that are encoded by separate genes that have been joined so that they are transcribed and translated as a single unit, producing a single polypeptide. Fusion proteins can be created in vivo, for example, as the result of a chromosomal rearrangement. The Bcl–abl fusion protein, which causes chronic myelogenous leukemia, is an example of such a fusion protein. Fusion proteins can also be created in vitro using recombinant DNA techniques. The fusion often consists of a protein that is being studied joined to one of a small number of proteins that have useful properties to aid in the study.
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Fusion Proteins
P. Riggs, in Encyclopedia of Genetics, 2001
Uses of Fusion Proteins
The technique of creating fusion proteins has been extended to other fusion partners, and additional uses have been developed for the fusion partner. Three of the most important uses of fusion proteins are: as aids in the purification of cloned genes, as reporters of expression level, and as histochemical tags to enable visualization of the location of proteins in a cell, tissue, or organism.
For purification, a protein that can be easily and conveniently purified by affinity chromatography is fused to a protein that the researcher wishes to study. A number of proteins and peptides have been used for this purpose, including staphylococcus protein A, glutathione-S-transferase, maltose-binding protein, cellulose-binding protein, chitin-binding domain, thioredoxin, strepavidin, RNaseI, polyhistidine, human growth hormone, ubiquitin, and antibody epitopes.
The proteins used most often as fusion partners for reporter constructs are β-galactosidase, luciferase, and green fluorescent protein (GFP). β-galactosidase has the advantage of numerous commercially available substrates, including some that produce a colored product and some that lead to the production of light. Luciferase and GFP both produce light, and can be visualized directly or quantitated using a luminometer or a fluorometer, respectively. GFP has an advantage in that it does not require a substrate, whereas luciferase requires its substrate, luciferin, as well as ATP, O2, and Mg2+. GFP emits green light when excited by blue or UV light, and in many cases can be used on live, intact cells and organisms.
A useful extension of fusion proteins as reporters is the two-hybrid system. In this method, two separate fusions are employed to test for interaction between two proteins, where binding of the two proteins brings together their fusion partners and results in activated transcription of a reporter gene.
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Technologies for making new vaccines
Ronald W. Ellis, ... Sohail Ahmed, in Vaccines (Sixth Edition), 2013
Fusion proteins
Recombinant fusion proteins containing multiple peptide sequences have been expressed as multiepitope vaccine antigens. A fusion protein containing the extracellular domains of two Streptococcus pneumoniae surface proteins has been evaluated in clinical studies.85 A recombinant Streptococcus pyogenes vaccine consisting of 26 M protein type-specific peptide sequences fused into four recombinant fusion proteins has been shown to stimulate responses to all 26 included S. pyogenes serotypes.86 Similarly, the expression of four of five antigens in the N. meningitidis serogroup B (MenB) vaccine as fusion proteins was undertaken to further increase immunogenicity, and this vaccine is being evaluated in clinical studies.87,88
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Antilymphocyte Globulin, Monoclonal Antibodies, and Fusion Proteins
Eileen T. Chambers, Allan D. Kirk, in Kidney Transplantation - Principles and Practice (Eighth Edition), 2020
Fusion Protein Structure and Function
Fusion proteins are molecules engineered from a single receptor targeting a ligand of interest fused to another protein that provides another salutary property. In transplantation, this secondary molecule is typically the Fc portion of an IgG molecule that gives the receptor an antibody-like half-life and/or opsonization properties.40–42 Fusion proteins also can involve the fusion of a specific toxin to a MAb to facilitate epitope-directed drug delivery.43 Fusion proteins are similar to MAbs in that they have a single homogeneous specificity and can be composed of human or humanized components, limiting their immune clearance and opening their use for prolonged administration. Currently, only a single fusion protein is approved for transplantation, belatacept, which is a mutated form of the receptor CTLA4 (CD152) fused to IgG Fc domain. Belatacept, along with notable examples of transplant-relevant fusion proteins in development, will be discussed subsequently.
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Primary Cutaneous Lymphomas
Richard T. Hoppe M.D., ... Ranjana Advani M.D., in The Lymphomas (Second Edition), 2006
Recombinant Fusion Proteins
Recombinant fusion proteins, such as the IL-2-diphtheria toxin fusion protein (Ontak, denileukin diftitox), incorporate growth factor-diphtheria toxin fusion proteins designed specifically to kill defined neoplastic cell populations. Denileukin diftitox has undergone a multicenter Phase III trial in patients with IL-2 receptor (CD25+)-expressing MF.85 Patients with intermediate or advanced stages of disease were included in the Phase III trial. The overall response rate was 30%, with complete response and partial response rates of 10% and 20%, respectively. The main complication related to a "capillary leak" syndrome may be ameliorated by pretreatment with corticosteroids.
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Membrane Fusion
A. Hinz, W. Weissenhorn, in Encyclopedia of Virology (Third Edition), 2008
Biosynthesis of Fusion Proteins
Class II fusion proteins comprise the fusion proteins from positive-strand RNA viruses such as the Togaviridae family, genus Alphaviruses (e.g., Semliki Forest virus (SFV)), and the Flaviviridae (e.g., Dengue, Yellow fever, and Tick-borne encephalitis virus (TBE)) (Table 1). Flaviviruses express the glycoprotein E that associates with a second precursor glycoprotein prM, while alphaviruses express two glycoproteins, the fusion protein El and the receptor-binding protein E2. E1 associates with the regulatory precursor protein p62. Both E-prM and E1-p62 heterodimerization are important for folding and transport of the fusion proteins. Cleavage of the fusion protein chaperones p62 and prM by the cellular protease furin in the secretory pathway is a crucial step in the activation of E and E1 fusion proteins.
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Viral surface glycoproteins in carbohydrate recognition
Jeffrey C. Dyason, Mark von Itzstein, in Microbial Glycobiology, 2010
2.3. Haemagglutinin esterase fusion protein
The HEF of influenza virus C is structurally very similar to HA found on the surface of influenza virus A and B, in that it is a homo-trimeric glycosylated surface protein. The major differences are in:
(i)
the receptor that is recognized, sialic acid-containing glycoconjugates are recognized by HA while 9-O-acetylated sialic acid-glycoconjugates are recognized by HEF; and
(ii)
the fact that HEF contains both a lectin function as well as a receptor-destroying enzyme, in contrast to influenza virus A and B that have two distinct proteins for these functions.
The receptor-destroying enzyme of HEF is an esterase and cleaves an O-acetate group from the 9′-position of sialic acids. The crystal structure of HEF was published in 1998 (Rosenthal et al., 1998) with the receptor-destroying enzyme active site being very similar in nature to a serine esterase and being completely separate to the receptor-binding site. Modelling experiments using a forced glycosidic angle torsion search have helped explain NMR results obtained recently within the von Itzstein group (Mayr et al., 2008) for both HEF and bovine coronavirus esterase. This led to the understanding of the essential pharmacophoric groups required for binding to the receptor-destroying enzyme active site and the knowledge that the aglycon group does not appear to be involved in substrate binding to this site. Similar haemagglutinin esterases (≈30% homology) have also been identified in corona and toroviruses (de Groot, 2006) and, although these viruses are not closely related to influenza virus C, an understanding of the structure and function of the haemagglutinin esterase will provide more information on the mechanism of cell recognition and entry.
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Immune Hypersensitivity
In Primer to the Immune Response (Second Edition), 2014
(2) Fusion proteins. Recombinant DNA technology has also been used to generate a fusion protein (FP) in which pieces of the Fel d 1 cat allergen were joined to a part of an HBV protein. This HBV fragment has already been shown to be a safe carrier protein that is fully able to induce T cell help. When injected into experimental animals, the recombinant FP antigen provoked a strong IgG response. The anti-FP IgG antibodies produced blocked the binding of anti-FP IgE to the native Fel d1 antigen, greatly reducing mast cell activation.
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Typing, grading, and staging of cases of tumor
Leon P. Bignold, in Principles of Tumors (Second Edition), 2020
(e) Neomolecules in tumors
Fusion proteins produced by chromosomal breaking and rejoining (see next subsection) are not amplified over normal components and so cannot be assayed, but the proteins which they stimulate expression of can be.
However, monitoring the mRNA of the fusion protein can be done and is standard management [30].
The main example is BCR/ABL, which is at the site of the Philadelphia chromosome translocation associated with chronic myeloid leukemia (see Section 2.6.10). The translocation allows the active breakpoint cluster gene (BCR) on chromosome 22q to activate the Abelson (ABL) tyrosine kinase gene on chromosome 9q. The gene product is a tyrosine kinase which is not affected by any physiological inhibitors. As a result, the gene has high constitutive activity, which causes excessive growth of the myeloid cells. The hyperproliferative cells are liable to further mutations due to reductions in DNA repair and genomic instability [31].
Other examples are the ALK fusion protein [32], ROS1 fusion gene [33], which has been found in a wide variety of cancer types including nonsmall cell lung cancer (NSCLC), gastric adenocarcinoma, colorectal and ovarian cancer, and NTRK fusion proteins [34].
Production of downstream proteins increased by the fusion protein can be detected [35,36].
A few are of some diagnostic value, e.g., and pathogenetic mutations in the same (e.g., in nonepithelial malignancies of the uterus) [37,38].
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Cytokines and Biologic Modifiers
In Immunology for Pharmacy, 2012
IL-1 as a Biologic Response Modifier
Fusion proteins, receptor antagonists, and monoclonal antibodies are used to neutralize the physiologic effects of soluble IL-1 or block the interactions with the receptor. Rilonacept is a fusion protein that contains the IL-1 receptor coupled with the Fc portion of immunoglobulin G (IgG). It binds and neutralizes soluble IL-1 before it can interact with its receptor. Canakinumab is a humanized monoclonal antibody directed at IL-1β. It blocks the effects of IL-1β and has no cross-reactivity with IL-1α or the IL-1 receptor. Anakinra is an IL-1 receptor antagonist that downregulates or blocks intracellular signaling. Many of these BRMs are used to treat patients with CAPS (Table 23-2).
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VPg
VPg could play a role in the circularization of the viral genome, possibly achieved through an interaction between the VPg-eIF4E/eIF(iso)4E complex and eIF4G/eIF(iso)4G, which itself interacts with PABP, or through the direct interaction between VPg-Pro and PABP (Leonard et al., 2004).
From: Advances in Virus Research, 2009
Related terms:
Capsid
Protease
RNA-dependent RNA Polymerase
Nested Gene
Virion
Genus
Open Reading Frame
RNA Synthesis
Virus Replication
Picornaviridae
View all Topics
Family Caliciviridae
Susan Payne, in Viruses, 2017
Translation
The calicivirus VPg protein (13–15 kDa) is much larger than the ~22 amino acid VPg of picornaviruses and it seems to play a larger role in replication. In addition to its role in genome replication, calicivirus VPg is essential for translation of viral RNA (Fig. 3.13). Removal of VPg from caliciviral RNA decreases infectivity as well as the ability of the RNA to support translation in cell-free systems. Conversely, addition of recombinant VPg to cell-free extracts inhibits both cap- and IRES-dependent translation suggesting that caliciviral VPg competes for initiation factors, effectively removing them from translation systems. VPg proteins from various caliciviruses have been shown to interact with eukaryotic initiation factors (eIF3, eIF4E, eIF4G), further supporting a role in translation.
Caliciviruses use a variety of protein expression strategies. In the case of vesiviruses and noroviruses, genome-length mRNA is used to express an ORF1 polyprotein that is proteolytically processed to produce the NS proteins NS1–NS7 (including NTPase, VPg, protease, and RdRp). A subgenomic mRNA is produced and contains one or two ORFs. The major capsid protein (VP1) is encoded by ORF2. The genome organization of the sapoviruses, lagoviruses, and neboviruses is a bit different as the capsid protein (VP1) is continuous with that of the NS proteins. However VP1 is also produced from a subgenomic mRNA. All caliciviruses encode a second, minor structural protein (VP2) from an ORF near the 3′ end of the genome. Murine noroviruses contain four ORFs.
Two different strategies are used to produce the minor capsid protein VP2 from the bicistronic mRNA. Noroviruses use leaky scanning (Fig. 3.14) for expression of VP2. In the case of FCV (vesivirus) and RHDV (lagosvirus), VP2 is expressed through RNA termination–reinitiation or stop–start (Fig. 3.14).
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Plant Virus Viromics
Roger Hull, in Plant Virology (Fifth Edition), 2014
b Cellular Factors Involved in Replication
Several host proteins interact with the VPg (Box 6.3) which, because of its intrinsically disordered nature, can be regarded as a hub protein of an interactive network.
Using the yeast two-hybrid system, Wittmann et al. (1997) found that the TuMV VPg interacted with the A. thaliana translational eukaryotic initiation factor (iso) 4E [eIF(iso)4E]; this interaction correlates with virus infectivity (Leonard et al., 2000, 2004). Since then, interaction between potyvirus VPg and initiation factors has been shown for several other potyviruses (Robaglia and Caranta, 2006; Truniger and Aranda, 2009); this interaction is important in plant resistance to the viruses (Chapter 11, Section IV, A). In the VPgs of all resistance-breaking isolates of different viruses, mutations have been localized to the central region, which is likely to be involved in eIF4E binding (Roudet-Tavert et al., 2007; Charron et al., 2008). Since different amino acids are substituted to generate resistant forms of eIF4E in different and even the same plant species, it is thought that the precise contact point between VPg and eIF4E needs to be optimized for each potyvirus (Charron et al., 2008). Most potyviruses specifically require one eIF4E isoform for their replication cycle but PVMV and TuMV can use both eIF4E and eIF(iso)4E (Ruffel et al., 2006; Jenner et al., 2010).
As noted above, potyviruses resemble animal picornaviruses in genome organization and polyprotein processing. Like picornaviruses, the VPg is uridylylated by the viral replicase (NIb) at tyrosine 66 (for PVBV); the uridylylation correlates with the nucleotide-binding capacity of the VPg (Puustinen and Mäkinen, 2004; Anindya et al., 2005).
The actual interaction with eIF4E/eIF(iso)4E occurs with precursor processing products 6K-VPg-Pro and VPg-Pro (see Figure 6.18A for potyviral polyprotein processing). The interaction with the 6K-VPg-Pro is found in cytoplasmic ER vesicles and that with VPg-Pro in the subnuclear region suggesting two different functions for VPg (Beauchemin et al., 2007).
As can be seen in Box 6.4, eIF4e interacts with eIF4G and, through eIF4G, with eIF4A, and the poly(A)-binding protein (PABP). All three of these factors [eIF4A (also termed AtRH8), eIF4G, and the PABP] are involved with potyviral replication (Nicaise et al., 2007; Dufresne et al., 2008b; Huang et al., 2010) presumably through the link with eIF4E (Plante et al., 2004). eIF(iso)4E is found, associated with the 6K2-VPg-Pro intermediate processing product and PABP, in virus-induced cytoplasmic vesicles and with VPg-Pro and PABP in the nucleolus (Beauchemin and Laliberté, 2007; Beauchemin et al., 2007). It is suggested that the whole initiation factor complex together with PABP and the viral intermediate processing product is involved in cytoplasmic potyviral replication and that the nucleolar form might be associated with antiviral defense (Taliansky et al., 2010).
The PABP is reported to also interact with the potyvirus RdRp (Wang et al., 2000) as also does the host heat shock 70 protein (heat shock cognate 70-3, Hsc70-3) (Dufresne et al., 2008a). As both Hsc70-3 and PABP are found located in virus-induced vesicles when co-expressed with 6K2-VPg-Pro, it is suggested that they may play an important role in the regulation of potyviral replication.
Eukaryotic elongation factor 1-alpha (eEF1A) interacts with TuMV RdRp and VPg-Pro in the virus-induced ER vesicles (Thivierge et al., 2008). Thus the vesicles contain at least three plant translation factors in addition to the viral replication proteins and may provide a mechanistic explanation for the coupling of viral RNA translation with viral RNA replication.
As well as the translation factors, potyviral VPg interacts with a cysteine-rich plant protein (termed potyvirus VPg-interacting protein, PVIP) that potentiates viral cell-to-cell movement (Dunoyer et al., 2004).
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Genome Composition, Organization, and Expression
Roger Hull, in Plant Virology (Fifth Edition), 2014
c VPg
There has been speculation that the potyviral VPg–eIF4E interaction (Box 6.3) facilitates cap-independent translation (Lellis et al., 2002; Gao et al., 2004; Thivierge et al., 2005) This is now considered to be unlikely (Pettit Kneller et al., 2006) as the VPg is unnecessary for efficient cap-independent translation. The 5′ UTR alone confers this function. However, the VPg enhances viral RNA translation and inhibits reporter mRNA translation both in vitro and in vivo (Khan et al., 2008; Eskelin et al., 2011). Poly(A)-binding protein increases the binding efficiency of TuMV VPg to eIFiso4 thereby leading to a rapid stable complex sequestering initiation complexes (Khan and Goss, 2012).
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Natural and Engineered Resistance to Plant Viruses, Part I
V. Truniger, M.A. Aranda, in Advances in Virus Research, 2009
D. Cap-binding ability of eIF4E/eIF(iso)4E mutants
There is no consensus on whether or not the VPg- and cap-binding domains of eIF4E overlap. The pepper pvr1 protein can bind neither VPg nor a cap analog, suggesting that the binding sites might overlap (Khan et al., 2006; Miyoshi et al., 2006; Yeam et al., 2007), but the pvr2 protein binds the cap normally despite its inability to bind VPg, suggesting that the overlap is not complete (Yeam et al., 2007). Lettuce eIF4E has similar binding affinities for a cap analog and VPg, but binding was shown to occur at different sites (Michon et al., 2006), whereas A. thaliana eIF(iso)4E binds TuMV VPg with higher affinity than capped RNA (Miyoshi et al., 2006). In several cases, cap analogs and VPg compete to bind eIF4E (Khan et al., 2006; Khraiwesh et al., 2008; Leonard et al., 2000). Therefore, the cap-binding ability of eIF4E/eIF(iso)4E does not necessarily correlate with its VPg-binding ability, since some mutant eIF4E/eIF(iso)4E proteins that confer resistance due to their limited interaction with VPg retain their cap-binding ability, while others do not (German-Retana et al., 2008). Because the precise contact point between VPg and eIF4E is optimized for each potyvirus, even in the same plant species (Charron et al., 2008), the various mutations in eIF4E/eIF(iso)4E may have different effects on cap binding.
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Bean Common Mosaic Virus and Bean Common Mosaic Necrosis Virus (Potyviridae)☆
Ramon Jordan, John Hammond, in Reference Module in Life Sciences, 2020
Properties of the genome and replication
The ssRNA genome, which has a VPg protein covalently linked to its 5′ end, is about 10,000 nt for BCMV and 9600 nt for BCMNV. The organization of the BCMV and BCMNV genomes is similar to other potyviruses, consisting of short untranslatable sequences at the 5′ and 3′ ends, and a single, long open reading frame (ORF). The ORF is translated into a single polyprotein: c. 3222 aa for BCMV and c. 3071 aa for BCMNV. The polyprotein undergoes co- and post-translational proteolytic processing by three viral-encoded proteinases to form ten individual gene products. Most of the polyprotein cleavage sites differ between BCMV and BCMNV, with the exception of the HC-Pro/P3 cleavage. The ten viral proteins (Fig. 2) include, in order from the 5′ end of the genome, P1 proteinase; helper component-proteinase (HC-Pro); P3; a 6 kDa protein (6K1); cylindrical inclusion (CI); a second 6 kDa protein (6K2); the nuclear inclusion "a" (NIa)-VPg protein; NIa-proteinase; nuclear inclusion "b" (NIb); and the CP. An additional protein is translated by a frameshift within the P3 gene, resulting in production of a fusion protein, P3N-PIPO. Genomic RNA replicates via production of a full-length negative-sense RNA.

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Fig. 2. Genome organization of BCMV and BCMNV. 5′, 5′ UTR; P1, P1 proteinase; HC-Pro, helper component-proteinase; P3, P3 protein; P3N-PIPO; 6K1, a 6 kDa protein; CI, cylindrical inclusion; 6K2, a second 6 kDa protein; NIa, nuclear inclusion "a", cleaved into VPg and Pro; VPg, genome-linked protein; Pro, proteinase; NIb, nuclear inclusion "b"; CP, coat protein; 3′,3′-UTR. P3N-PIPO is expressed as a result of a frameshift within the P3 ORF.
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Structural Biology of Noroviruses
B.V. Venkataram Prasad, ... M.K. Estes, in Viral Gastroenteritis, 2016
5.1 VPg
Similar to picornaviruses and as demonstrated in animal caliciviruses, VPg (by inference in NoVs) is covalently linked to the genomic RNA (Thorne and Goodfellow, 2014). However, unlike picornavirus VPg, which is only about ∼2 kDa in size, VPg in caliciviruses is significantly larger (12–15 kDa). The calicivirus genomes do not have a capped 5′-end, like cellular RNAs, or an internal ribosome entry site (IRES) as in picornaviral RNA, for RNA translation. Studies on animal caliciviruses and NoVs have attributed a dual role to this protein. First, VPg acts as a "cap substitute" and mediates translation initiation of viral RNA based on the observations that m7-GTP cap can substitute for VPg to confer infectivity in vitro to synthesized FCV RNA (Sosnovtsev and Green, 1995), and that it can bind directly to initiation factor eIF4E (Daughenbaugh et al., 2003, 2006; Goodfellow et al., 2005). Second, analogous to picornavirus VPg, the NoV VPg has a priming function during RNA replication based on the observation that VPg is uridylylated at a conserved Tyr residue by the viral RdRp followed by elongation in the presence of RNA (Belliot et al., 2008; Han et al., 2010; Mitra et al., 2004; Royall et al., 2015; Chung et al., 2014).
Currently, there is no structural information on full-length VPg for any calicivirus. However, NMR structures of the central core of VPg, consisting of about ∼55 residues, from FCV (Leen et al., 2013), porcine sapovirus (PSV) (Hwang et al., 2015), and murine NoV (MNV) (Leen et al., 2013) have been determined. The N-terminal and the C-terminal regions flanking the central core are considered mostly disordered. The VPg core structures of FCV and PSV are very similar with a well-defined three-helical bundle, whereas that of MNV consists of only two of these helical segments (Fig. 3.1.4A). The Tyr residue within a conserved DDEYDEW motif is suggested to function as a nucleotide acceptor for viral replication and translation (Belliot et al., 2008; Han et al., 2010; Mitra et al., 2004). In all the three structures, the location of this residue, which is fully solvent exposed, is conserved. Although currently there are no structural studies on calicivirus VPg-RdRp, crystallographic structures of VPg-RdRp complex of foot-and-mouth disease virus (a picornavirus) both in the presence and absence of oligoadenylate substrate have been determined, and provide mechanistic details of how VPg interacts with RdRp in carrying out its priming function (Ferrer-Orta et al., 2006). Given that calicivirus VPg is significantly larger than picornavirus VPg, it remains to be seen how much of the structural details of the interactions between VPg and RdRp in caliciviruses remain similar.

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Figure 3.1.4. Calicivirus VPg and protease structures.
(A) NMR structures of the VPg core of MNV (left) (PDB id: 2M4G), FCV (middle) (PDB id: 2M4H), and porcine Sapovirus (right) (PDB id: 2MXD). The exposed Tyr residue that is be uridylylated by the RdRp in each structure is shown in stick representation. (B) Cleavage sites in the NV polyprotein, from the N- to C-terminal, along with the surrounding N-terminal P1-P4 and C-terminal P1′-P4′ residues. (C) Left. Cartoon representation of the NV protease structure (PDB id: 4IN1), the N-terminal and C terminal domains are shown in blue and cyan, respectively. The catalytic triad is shown in red. Right. Surface representation of the protease structure showing the locations of the S1 (blue), S2 (green), and S4 (gold) pockets, and the oxyanion hole (pink), with respect to the active site (red) (see Zeitler et al., 2006; Muhaxhiri et al., 2013). The substrate binding cleft between the two β-barrel domains is shown by a black dashed line. (D) Coordinated structural changes in the S2 (top) and S4 (bottom) pockets before (left) (PDB id: 2FYQ) and after (right) (PDB id: 4IN2) substrate binding. The substrate binding pockets are depicted in the same color as in Fig. 3.1.4C, right. Substrate is shown as yellow sticks.
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Dancing Protein Clouds: Intrinsically Disordered Proteins in Health and Disease, Part B
Pushpendra Mani Mishra, ... Chayan Kanti Nandi, in Progress in Molecular Biology and Translational Science, 2020
10.3 Intrinsic disorders in viral genome-linked proteins
In few viruses, a protein named viral genome-linked protein (VPg) is bound to 5′ end of their RNA genome through a phosphodiester bond formed between the hydroxyl group of Thr/Ser/Tyr residues and 5′ phosphate group of RNA.260–262 VPg's are highly diverse in terms of their size and sequence. For example, in Comoviridae and Picornaviridae members it is 2–4 kDa, Caliciviridae, Sobemoviruses, and Potyviridae members it is 10–26 kDa, while it is up to 90 kDa in Birnaviridae members.263 VPg plays a key role in major steps of the viral life cycle, such as cell-cell movement, replication, and translation. Since VPg performs these crucial functions either in its mature or precursor form, VPg precursor processing represents one of the regulatory mechanisms of its multi-functionality.262 The multitude of interactions with different viral and host proteins define VPg multifunctional role. The different interactions made by VPgs are: VPg to itself, cylindrical inclusion helicase, cylindrical inclusion protein, nuclear inclusion protein b, helper component protease, coat protein or eukaryotic translation initiation factors eIF4A, eIF4E, eIF3, and eIF4G, and the poly(A)-binding protein.262,264–272 Poly-functionality and binding promiscuity of VPs' at least to some extent is due to its intrinsically disordered nature. Intrinsically disordered nature of VPg was reported for many viruses through their individual protein characterization. These viruses are: rice yellow mottle virus (RYMV), Sesbania mosaic virus (SeMV), potato virus Y (PVY), potato virus A (PVA), and lettuce mosaic virus (LMV).262,273–276 The computational analysis showed that functionally important disordered VPg representative of viral diversity includes four members of the Caliciviridae family, six potyviruses and six sobemoviruses.276 The disordered VPg components associated with the regulation of enzymatic activity in different viruses273,277 in addition to performing specific regulation and transportation of viral RNA from one cell to another.278
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Theiler's Virus
H.L. Lipton, ... N. Knowles, in Encyclopedia of Virology (Third Edition), 2008
Viral RNA Replication
Cardiovirus replication is similar to that of other picornaviruses. Following entry, VPg is removed from the 5′ end of the RNA, and the RNA is directly translated using cellular factors. The viral genomic RNA (plus-sense), is then transcribed into negative-strand copies, and each one is used as template for reiterative synthesis of ∼25–50 plus-sense RNAs identical to the genome of the virus. An RNA structure located within the VP2 sequence of TMEV is necessary for RNA replication, and is referred to as the cis-acting replicative element (CRE). The CRE functions as a template for uridylylation of viral protein 3B (VPg) forming VPgpUpUOH which primes positive-strand RNA synthesis. Viral protein 3D is the RNA-dependent RNA polymerase which catalyzes both of these processes.
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Cardioviruses (Picornaviridae)
Douglas G. Scraba, Ann C. Palmenberg, in Encyclopedia of Virology (Second Edition), 1999
Synthesis of Components for Progeny Virions
Once in the cellular cytoplasm, the infecting viral RNA (with its VPg removed) acts as messenger RNA. The translation of this RNA into a polyprotein and the proteolytic processing of the polyprotein have been discussed. The infecting RNA must also be able, at some stage, to free itself from the translation machinery and act as a template for the synthesis of a complementary (minus-strand) RNA. How this is accomplished is not known. The minus-strand RNA acts as a template for the synthesis of progeny plus strands (virion RNAs), with several plus strands being synthesized simultaneously. These structures can be isolated from endoplasmic membrane fractions of infected cells, and are called replicative intermediates (RIs; Fig. 3). The proteins encoded by the P2 and P3 region of the viral genome are responsible for RNA replication: VPg initiates each newly synthesized molecule, plus or minus strand, and 3Dpol is the elongation polymerase. There is a dramatic asymmetry in RNA synthesis, with a large excess of plus strands and no evidence for RIs composed of a plus-strand template and nascent minus strands. The mechanism(s) by which RNA synthesis is regulated is not understood.

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Figure 3. Regulation of cardiovirus replication. (A) At early times after infection (0–5 h), the cellular phosphotyrosine phosphatase has easy access to the nascent plus-strands of viral RNA in RI replicative intermediate structures. It removes the 5′-VPg proteins from these RNAs, making them templates for continuing viral protein biosynthesis. (B) At later times (5–10 h), 14S pentamers accumulate and compete with the phosphatase for the VPg RNAs. As time goes on, more progeny plus-strand RNAs from the RIs are packaged into progeny virions, and fewer become mRNAs.
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Virion
CEVs induce polymerization of actin to form filaments that effect the direct transfer of CEVs to adjacent cells.
From: Tropical Infectious Diseases (Third Edition), 2011
Related terms:
Capsid
Bacteriophages
Monospecific Antibody
Cell Membrane
Host Cell
Genus
Virus Nucleocapsid
Virus Particle
Human Immunodeficiency Virus
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Tombusviridae
In Virus Taxonomy, 2012
Virion properties
Morphology
Virions are approximately 30 nm in diameter and exhibit icosahedral symmetry (Figure 16). Detailed structure of virions is not known. Based on CP sequence similarity, it is predicted that the capsid is structurally similar to the T=3 capsids of sobemoviruses.

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Figure 16. (Left) Diagrammatic representation of a particle of MCMV. VP1, VP2 and VP3 correspond to the three conformational states of the CP subunit. (Right) Negative contrast electron micrograph of MCMV virions. The bar represents 100 nm.
Physicochemical and physical properties
Mr of virions is 6.1×106; S20,w is 109S; buoyant density in CsCl is 1.365 g cm−3. Virions are insensitive to ether, chloroform and non-ionic detergents. Virions are stable in vitro for up to 33 days and the thermal inactivation point of virions is between 80–85 °C. Virions are stable at pH 6 and lower. Virions are stabilized by divalent cations.
Nucleic acid
Virions contain a single molecule of infectious linear positive sense ssRNA. The RNA is 4437 nt in length. The 5' end of the RNA is probably uncapped The RNA does not contain a 3'-terminal poly(A) tract. Either a 1470 or an 1100 nt sgRNA is also packaged into virions at a very low level.
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Barnaviridae
In Virus Taxonomy, 2012
Virion properties
Morphology
Virions are bacilliform, non-enveloped and lack prominent surface projections. Typically, virions are 19×50 nm, but range between 18 and 20 nm in width and 48 and 53 nm in length (Figure 1). Optical diffraction patterns of the virions resemble those of virions of Alfalfa mosaic virus, suggesting a morphological subunit diameter of about 10 nm and a T=1 icosahedral symmetry.

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Figure 1. Negative contrast electron micrograph of particles of an isolate of Mushroom bacilliform virus. The bar represents 100 nm.
Physicochemical and physical properties
Virion Mr is 7.1×106, buoyant density in Cs2SO4 is 1.32 g cm−3. Virions are stable between pH 6 and 8 and ionic strength of 0.01 to 0.1M phosphate, and are insensitive to chloroform.
Nucleic acid
Virions contain a single linear molecule of a positive sense ssRNA, 4.0 kb in size. The complete 4009 nt sequence of mushroom bacilliform virus (MBV) is available. The RNA has a linked VPg and appears to lack a poly(A) tail. RNA constitutes about 20% of virion weight.
Proteins
Virions contain a single major CP of 21.9 kDa. There are probably 240 molecules in each capsid.
Lipids
None reported.
Carbohydrates
None reported.
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Ribonucleases - Part B
James R. Smiley, ... Holly A. Saffran, in Methods in Enzymology, 2001
Regulation of vhs Activity during Infection
vhs significantly destabilizes viral mRNAs in infected cells, and even targets it own mRNA for destruction in the RRL system.3 These observations raise an interesting question; how do HSV mRNAs accumulate to high levels in infected cells in the face of vhs action? This question is especially pertinent at late times postinfection, when high levels of new vhs protein are made for incorporation into progeny virions.5 M. Fenwick and colleagues26,27 proposed that the solution lies in temporal control of vhs activity during infection. Specifically, Fenwick suggested that a newly synthesized viral protein partially dampens the activity of vhs delivered by the infecting virion, thereby allowing viral mRNAs to accumulate after host mRNAs have been degraded. We have shown that vhs specifically binds to the virion transcriptional activator VP16,28 and provided genetic evidence that this interaction downregulates vhs activity.29 VP16 is well known for its ability to activate transcription of the viral immediate-early genes, through its association with the host factors Oct1 and host cell factor (HCF).30 We found that viral mRNAs are grossly destabilized during infection in the absence of VP16, leading to virtually complete translational arrest midway through the infection cycle.29 This defect was corrected by transcriptionally incompetent forms of VP16 that retain the ability to bind vhs, and was eliminated by inactivating the vhs gene of the VP16 null mutant. Moreover, cells constitutively expressing VP16 were rendered resistant to virion-induced shutoff mediated by superinfecting HSV. Taken in combination, these results revealed a major and unanticipated posttranscriptional regulatory function of VP16, and provided insight into how HSV evades one of its own host shutoff mechanisms. However, it is not