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Expression and characterization of poliovirus proteins 3BVPg, 3Cpro, and 3Dpol in recombinant baculovirus-infected Spodoptera frugiperda cells.

As an initial step toward investigating the roles of poliovirus proteins in viral RNA replication, a baculovirus expression system was used to produce poliovirus proteins from the P3 region. Spodoptera frugiperda (Sf9) cells were infected with a recombinant baculovirus, vETL-PoV3A*BCD, which contains cDNA coding for poliovirus proteins 3D, 3C, 3B, and a portion of 3A protein sequence. Immunofluorescence microscopy revealed that the majority of 3D (polymerase) was in the cytoplasm of recombinant baculovirus-infected Sf9 cells. In the same cells, the 3C (protease) and 3B (VPg) proteins appeared to be located in distinct subcellular regions, possibly membrane structures, suggesting that the expressed polyprotein was cleaved to generate mature proteins. Processing of the polypeptide was confirmed by immunoblot analysis which demonstrated that 3Cpro sequences were active in cleavage of the polyproteins 3A*BCD and 3CD. Over 95% of the 3D sequences accumulated in the form of mature 3Dpol, with only low levels of 3CD remaining. The majority of 3Dpol remained in the supernatant after low speed centrifugation of sonicated cells. The 3Dpol had RNA-dependent RNA polymerase activity as measured by elongation of an oligo(U) primer using a poly(A) template. The protein 3CDpro was active in cleaving P1 protein. The yield and activities of the poliovirus proteins expressed will facilitate future biochemical studies.

Animals↗

Pestivirus bovine viral diarrhea virus polypeptides: identification of new precursor proteins and alternative cleavage pathways.

The genome of pestivirus bovine viral diarrhea virus (BVDV) contains a single 11,964 nt long open reading frame (ORF) that is capable of encoding a 449 kDa putative polyprotein. Although previous studies have described many virus-coded polypeptides that are believed to arise by post- and/or co-translational proteolytic processing in infected cells, there are two separate regions in the ORF for which no polypeptide products could be identified. In the present study using site specific antisera, we identified two new large proteins of Mr 175 and 172 kDa which encompass two previously described smaller precursor proteins, p125 and p133, respectively. These two large precursor proteins together with two other previously described proteins p22 and gp118 (Mr approx. 84 kDa; unglycosylated) account for the predicted Mr of the putative 449 kDa polyprotein precursor. Furthermore, we discovered three additional polypeptides of Mr 168, 96 and 72 kDa encoded by the last third of the genome. These proteins may arise by an alternative cleavage pathway of the precursor protein p172. A modified and updated map of BVDV ORF incorporating the above findings is presented.

Animals↗

Modification of infectious bursal disease virus antigen VP2 for cell surface location fails to enhance immunogenicity.

The host protective antigen gene VP2 of infectious bursal disease virus (IBDV) was genetically modified and expressed by recombinant fowlpox viruses (rFPV). To achieve cell surface localization, VP2 was expressed as a hybrid protein with signal sequence and membrane anchors of influenza virus hemagglutinin or neuraminidase. Native VP2 was expressed as VP2 alone or as self-processing VP2-VP4-VP3 polyprotein for coexpression of IBDV structural proteins. VP2 hybrid protein containing the carboxy-terminal membrane anchor sequence of influenza virus hemagglutinin was located on the cell surface and was N-glycosylated. The expression of VP2 fused to the N-terminal signal/anchor sequence of influenza virus neuraminidase led to cell lysis and the VP2 protein remained mainly unglycosylated. Cell surface localization of VP2 reduced immunogenicity (antibody induction) and abolished protection in poultry in comparison with the native VP2 expressed by FPV as VP2 alone or as the self-processing VP2-VP4-VP3. Vaccination of poultry with rFPV expressing native VP2 protein alone provided better protection from IBDV infection than VP2 derived from the VP2-VP4-VP3 polyprotein.

Animals↗

Characterization of revertants of a Sindbis virus 6K gene mutant that affects proteolytic processing and virus assembly.

Alphaviruses of the Togaviridae encode a small hydrophobic polypeptide of 55 amino acids, noted as the 6K protein, that is synthesized as part of a polyprotein containing the sequences of the two major transmembranal viral structural glycoproteins. Mutations, insertions and deletions in the 6K appear to selectively interfere with the final stages of virus assembly and budding, producing aberrant, multi-cored infectious viruses. In addition, some of these mutations were pleiotropic and much more inhibitory to virus formation. One of the latter, a substitution of alanine in the wild-type Sindbis virus 6K gene by arginine, has been studied further and shown to interfere with normal proteolytic processing of the polyprotein. Cells infected with this mutant but not the wild-type virus also displayed viral antigens in nuclear membranes and released fragments of membranes into the cell culture media. A revertant, obtained by enrichment for a faster growing strain, 'suppressed' these defects and genetic mapping showed that the arginine codon had been modified to encode a methionine. However, the sequence of the 6K protein in this revertant was not wild-type and the revertant was still defective in assembly as demonstrated by formation of aberrant particles. A complete restoration of wild-type particle formation for this revertant could be effected by modifying the E2 glycoprotein sequence.

Animals↗

Coding sequences of both genome segments of a European 'very virulent' infectious bursal disease virus.

The sequences of segment A (encoding the VP2-VP4-VP3 polyprotein and VP5) and segment B (encoding VP1) of a recent, 'very virulent' (VV) European isolate (UK661) of infectious bursal disease virus (IBDV), a birnavirus, have been determined. There are 26 to 36 amino acid substitutions compared to any other type I IBDV within the segment A polyprotein (of these, 15 are unique) and about 50 substitutions within VP1 (of which 16 are unique). There is more variation compared to classical and antigenic variant viruses, of both virulent and attenuated phenotype, in VP1, VP3 and VP4 than in VP2, even though the latter has previously been identified as the most variable protein between different strains of type I IBDV. In VP3 and VP4, UK661 is the most diverged type I IBDV. Thus the origin of the virus is unclear. It is possible that strong functional constraints have preferentially maintained the primary structure of VP2, though the possibility of recombination cannot be excluded. There are no clear candidate mutations to account for the enhanced virulence of the VV IBDV. Polymerase motifs are well conserved in VP1 but there is an amino acid substitution next to the predicted active-site serine of the viral protease (VP4). In addition, there is a conservative substitution close to the postulated VP2-VP4 cleavage site. It is also now apparent that sequences of IBDV segment B (the segment encoding the RNA polymerase) do not group according to serotype (specified by the capsid proteins encoded on segment A), indicating that segment reassortment has occurred.

Amino Acid Sequence↗

Nucleotide sequence of the coat protein genes of citrus mosaic virus.

The sequence of the 3'-terminal 2,201 nucleotides of RNA2 of citrus mosaic virus (CiMV) was determined. The sequence contains a long open reading frame (ORF) of 1989 nucleotides in the virus-sense strand and at 3' untranslated region of 212 nucleotides upstream of a poly(A) tail. The N-terminal amino acid sequence of the two coat proteins was determined by Edman degradation and the corresponding coding regions were identified in the polyprotein. The larger coat protein with Mr 48,122 is encoded upstream of the smaller one with Mr 24,172. The coat proteins are apparently cleaved from the polyprotein at an Arg-Gly and a Thr-Asn bond. Although CiMV has properties in common with the comoviruses and nepoviruses, there is no significant sequence homology between the coat proteins of CiMV and those of either group. Furthermore, the coat proteins of CiMV lack homology with those of strawberry latent ringspot virus (SLRSV), which has been reported to be more distantly related to the como- and nepoviruses. This lack of homology distinguishes CiMV from the como- and nepoviruses, SLRSV and other viruses.

Amino Acid Sequence↗

Sequence of the region coding for virion proteins C and E2 and the carboxy terminus of the nonstructural proteins of rubella virus: comparison with alphaviruses.

The sequence of the 3' 4508 nucleotides (nt) of the genomic RNA of the Therien strain of rubella virus (RV) was determined for cDNA clones. The sequence contains a 3189-nt open reading frame (ORF) which codes for the structural proteins C, E2 and E1. C is predicted to have a length of 300 amino acids (aa). The N-terminal half of the C protein is highly basic and hydrophilic in nature, and is putatively the region of the protein which interacts with the virion RNA. At the C terminus of the C protein is a stretch of 20 hydrophobic aa which also serves as the signal sequence for E2, indicating that the cleavage of C from the polyprotein precursor may be catalyzed by signalase in the lumen of the endoplasmic reticulum. E2 is 282 aa in length and contains four potential N-linked glycosylation sites and a putative transmembrane domain near its C terminus. The sequence of E1 has been previously described [Frey et al., Virology 154 (1986) 228-232]. No homology could be detected between the amino acid sequence of the RV structural proteins and the amino acid sequence of the alphavirus structural proteins. From the position of a region of 30 nt in the RV genomic sequence which exhibited significant homology with the sequence in the alphavirus genome at which subgenomic RNA synthesis is initiated, the RV subgenomic RNA is predicted to be 3346 nt in length and the nontranslated region from the 5' end of the subgenomic RNA to the structural protein ORF is predicted to be 98 nt. In a different translation frame beginning at the 5' end of the RV nt sequence reported here is a 1407 nt ORF which is the C terminal region of the nonstructural protein ORF. This ORF overlaps the structural protein ORF by 149 nt. A low level of homology could be detected between the predicted amino acid sequence of the C-terminus of the RV nonstructural protein ORF and the replicase proteins of several positive RNA viruses of animals and plants, including nsp4 of the alphaviruses, the protein encoded by the C-terminal region of the alphavirus nonstructural ORF. However, the overall homology between RV and the alphaviruses in this region of the genome was only 18%, indicating that these two genera of the Togavirus family are only distantly related. Intriguingly, there is a 2844-nt ORF present in the negative polarity orientation of the RV sequence which could encode a 928-aa polyprotein.

Alphavirus↗

Purification of enzymatically active poliovirus proteinase 3C produced in Escherichia coli.

A viral protein 3C of the poliovirus (PV) Sabin 2 strain, a possible core region of the viral proteinase, was expressed in Escherichia coli using a recombinant DNA technology. The protein was recovered as a soluble protein from the insoluble protein fraction of the bacterial lysate, and was purified by a simple procedure with column chromatography. The viral capsid precursor P1 (1ABCD) of the PV Sabin 3 strain, which had been similarly produced in E. coli, was mixed with the purified or crude recombinant 3C. Immunoblotting assay with monoclonal antibodies specific to capsid proteins 1C (VP3) and 1D (VP1) of the PV Sabin 3 strain revealed that the in vitro reaction products contained 1C (VP3), 1D (VP1) and 1ABC (VP0-VP3). The data indicated that processing of the polyprotein P1 by the recombinant 3C proceeded properly in vitro, although an undigested product, 1ABC, is always detected in the reaction mixture. The results strongly suggest that, in addition to a protein 3CD, the 3C protein itself is also catalytically active in the processing of the viral capsid precursor polyprotein P1.

3C Viral Proteases↗

Sequence analysis of cloned dengue virus type 2 genome (New Guinea-C strain).

Sequences totalling 5472 nucleotides (nt) from four complementary DNA (cDNA) clones of the dengue virus type 2 (DEN-2) RNA (New Guinea strain, NGS-C) have been reported previously [Yaegashi et al., Gene 46 (1986) 257-267; Putnak et al., Virology 163 (1988) 93-103]. This report describes the complete nucleotide sequence, with the exception of about 7 nt at the 5'-noncoding region, of this RNA genome derived from several cDNA clones. It is 10,723 nt in length and contains a single long open reading frame of 10,173 nt, encoding a polyprotein of 3391 amino acids. The genomic organization is similar to that of other flaviviruses that have recently been reported. Among the three DEN-2 strains - the Jamaica genotype (DEN-2JAM), the DEN-2NGS-C, and the S1 candidate vaccine strain derived from Puerto Rico (PR)-159 isolate (DEN-2S1) - which have been sequenced to date, the amino acid sequences of the polyproteins bear 94%-99% similarity. When the amino acid sequences of DEN-2NGS-C are compared with those of the other two strains, the variations are greater in the DEN-2S1 than in the DEN-2JAM. When DEN-2 and DEN-4 are compared, the overall amino acid identities range from 30% to 80% in both the structural and nonstructural proteins; whereas between DEN-2 and DEN-1, they range from 68% to 79% in the region encoding the structural proteins and the nonstructural protein NS1.

Amino Acid Sequence↗

Generation of long flavivirus expression cassettes by in vivo recombination and transient dominant selection.

Assembly of expression cassettes coding for large segments of viral polyproteins is often complicated or impossible due to the instability of the resulting recombinant (re-) plasmids during propagation in Escherichia coli. Using the transient dominant selection approach described for the construction of vaccinia virus recombinants (re-VV), we have constructed several intermediate vectors and developed a procedure which enables direct assembly of long expression cassettes in the VV genome by in vivo recombination and does not require preliminary assembly of long cassettes in intermediate plasmids, thus eliminating the instability problems. The procedure was used to construct re-VV carrying fragments of the West Nile (WN), Murray Valley encephalitis (MVE), tick-borne encephalitis (TBE) and dengue type-2 (DEN2) viral genomes. Using this procedure, we have assembled a WN expression cassette which represents 86% of the WN genome and codes for 91% of its polyprotein and constitutes the longest flavivirus (FV) expression cassette inserted so far into the VV genome. Analysis of FV protein expression from the obtained recombinants indicates that recombination occurs with a high degree of specificity and the ORF remains intact. The procedure described offers a possible approach for the assembly of infectious cDNA clones.

Base Sequence↗

The genomic map of hepatitis A virus: an alternate analysis.

Recently Najarian et al. reported a complete cDNA sequence of the genomic RNA of hepatitis A virus (HAV) and the amino acid sequence inferred from it. As a picornavirus, HAV contains a single-stranded plus-sense RNA encoding a single 'polyprotein' which is post-translationally cleaved to yield the mature structural and non-structural proteins. In order to identify putative cleavage sites a combined function of predicted secondary structure and hydropathy was calculated by Najarian et al. for the polyproteins of HAV and poliovirus type 1 (Mahoney) (PV-1) and the two plots were aligned on the basis of a short homology in capsid protein VP3. Several of the proteins thereby predicted fail to conserve features found in all other picornaviruses that have been examined and, indeed, on the basis of these predictions HAV would hardly be a picornavirus. By an alternate analysis utilizing the computer programs FASTP and PRTALN we find that a putative protein processing map which does preserve these features can be constructed.

Chromosome Mapping↗

Photocontrol and processing of LHCP II apoprotein in Euglena: possible role of Golgi and other cytoplasmic sites.

Like other green photosynthetic eukaryotes, cells of Euglena gracilis var. bacillaris and strain Z contain a light-harvesting chlorophyll a/b complex associated with photosystem II. In Euglena, the formation of the 26.5 kDa principal light-harvesting chlorophyll a/b binding protein of photosystem II (LHCP II) has a number of unusual features. The precursors to LHCP II are large polyproteins containing multiple copies of LHCP II, and photocontrol of their formation is largely translational. Under conditions favoring LHCP II accumulation in the thylakoids, a reaction with anti-LHCP II antibody can be observed in the Golgi by immunogold electron microscopy. The timing of the immunoreaction in the Golgi in synchronous cells and in cells undergoing normal light-induced chloroplast development suggests that the nascent LHCP II passes through the Golgi on the way to the thylakoids. The compartmentalized osmiophilic structure (COS) also shows an immunoreaction. These observations, and other discussed in this paper, suggest that light permits translation of polyprotein LHCP II precursors on cytoplasmic ribosomes of the rough endoplasmic reticulum (ER) and that these pass through the ER to the Golgi where, presumably, further modifications take place. Since an LHCP II immunoreaction is found in Golgi vesicles, these may transport the nascent LHCP II to the plastid and facilitate its uptake.

Amino Acid Sequence↗

Expression and processing of hepatitis C virus structural proteins in Pichia pastoris yeast.

Development of heterologous systems to produce useful HCV vaccine candidates is an important part of HCV research. In this study different HCV structural region variants were designed to express the first 120 aa, 176 aa, 339 aa, and 650 aa of HCV polyprotein, and aa 384 to 521, or aa 384-605 or aa 384-746 of HCV E2 protein fused to the leader sequence of sucrose invertase 2 allowing the secretion of recombinant E2 proteins. Low expression levels were observed for HCV core protein (HCcAg) variants expressing the first 120 aa and 176 aa (HCcAg.120 and HCcAg.176, respectively). Higher expression levels were observed when HCcAg was expressed as a polypeptide with either E1 or E1 and E2 proteins. In addition, HCcAg was processed to produce two antigenic bands with 21 and 23kDa (P21 and P23, respectively) when expressed as a polypeptide with HCV E1 and E2 proteins. Results also suggest E1 processing in the context of HCcAg.E1.E2 polyprotein. On the other hand, E2.521, E2.605, and E2.680 were efficiently excreted to the culture medium. However, the entire E2.746 variant predominantly localized in the insoluble fraction of ruptured cells. Results suggest that the hydrophobic C-terminal E2 region from aa 681 to 746 is critical for intracellular retention of recombinant E2.746 protein in Pichia pastoris cells. Endo H or PNGase F treatment suggests that E2.746 was modified with high-mannose type oligosaccharides in P. pastoris. These data justify the usefulness of P. pastoris expression system to express HCV structural viral proteins which may be useful targets for HCV vaccine candidates.

Antigens, Viral↗

Structural biology of the dengue virus NS2B-NS3 protease as a target for antiviral drug development.

Dengue is the most common global problem in recent times, particularly in tropical and subtropical areas, yet antivirals for therapy or prophylaxis are lacking. Millions of people are affected by this dengue virus, but no proper medication is available yet to cure this disease. One polyprotein that is encoded by the DENV genome is converted into structural and non-structural proteins that are necessary for viral pathogenesis and replication. Among these, the non-structural protein complex NS2B-NS3 is essential for viral polyprotein processing, replication, and host innate immune response control. It acts as a trypsin-like serine protease. The NS2B/NS3 protease is a key enzyme involved in viral replication and serves as a major target for drug development against the dengue virus. The NS3 protease has a conserved catalytic triad (His-Asp-Ser), whereas NS2B serves as an essential cofactor that stabilizes the active conformation of the enzyme and aids in substrate recognition. By disrupting interferon signalling pathways, the NS2B-NS3 protease not only aids in viral replication but also makes immune evasion easier. The compound that inhibits the action of this enzyme could be pioneering in the antiviral drug discovery process. This article provides a comprehensive overview of the detailed structural information of the viral protease (NS2B/NS3) enzyme with the mechanistic role of this enzyme, and highlights various inhibitors related to the NS2B/NS3 protease. A more thorough comprehension of this protease could facilitate the logical development of potent antiviral medications to prevent dengue infection.

Dengue↗

Fast folding of the two-domain semliki forest virus capsid protein explains co-translational proteolytic activity.

The capsid protein of Semliki Forest virus constitutes the N-terminal part of a large viral polyprotein. It consists of an unstructured basic segment (residues 1-118) and a 149 residue serine protease module (SFVP, residues 119-267) comprised of two beta-barrel domains. Previous in vivo and in vitro translation experiments have demonstrated that SFVP folds co-translationally during synthesis of the viral polyprotein and rapidly cleaves itself off the nascent chain. To test whether fast co-translation folding of SFVP is an intrinsic property of the polypeptide chain or whether folding is accelerated by cellular components, we investigated spontaneous folding of recombinant SFVP in vitro. The results show that the majority of unfolded SFVP molecules fold faster than any previously studied two-domain protein (tau=50 ms), and that folding of the N-terminal domain precedes structure formation of the C-terminal domain. This shows that co-translational folding of SFVP does not require additional cellular components and suggests that rapid folding is the result of molecular evolution towards efficient virus biogenesis.

Capsid↗

Myomesin is a molecular spring with adaptable elasticity.

The M-band is a transverse structure in the center of the sarcomere, which is thought to stabilize the thick filament lattice. It was shown recently that the constitutive vertebrate M-band component myomesin can form antiparallel dimers, which might cross-link the neighboring thick filaments. Myomesin consists mainly of immunoglobulin-like (Ig) and fibronectin type III (Fn) domains, while several muscle types express the EH-myomesin splice isoform, generated by the inclusion of the unique EH-segment of about 100 amino acid residues (aa) in the center of the molecule. Here we use atomic force microscopy (AFM), transmission electron microscopy (TEM) and circular dichroism (CD) spectroscopy for the biophysical characterization of myomesin. The AFM identifies the "mechanical fingerprints" of the modules constituting the myomesin molecule. Stretching of homomeric polyproteins, constructed of Ig and Fn domains of human myomesin, produces a typical saw-tooth pattern in the force-extension curve. The domains readily refold after relaxation. In contrast, stretching of a heterogeneous polyprotein, containing several repeats of the My6-EH fragment reveals a long initial plateau corresponding to the sum of EH-segment contour lengths, followed by several My6 unfolding peaks. According to this, the EH-segment is characterized as an entropic chain with a persistence length of about 0.3nm. In TEM pictures, the EH-domain appears as a gap in the molecule, indicating a random coil conformation similar to the PEVK region of titin. CD spectroscopy measurements support this result, demonstrating a mostly non-folded conformation for the EH-segment. We suggest that similarly to titin, myomesin is a molecular spring, whose elasticity is modulated by alternative splicing. The Ig and Fn domains might function as reversible "shock absorbers" by sequential unfolding in the case of extremely high or long sustained stretching forces. These complex visco-elastic properties of myomesin might be crucial for the stability of the sarcomere.

Circular Dichroism↗

Polymorphism of gp15/400 allergen gene of W. bancrofti from different regions of India endemic for lymphatic filariasis.

Nematode polyprotein allergens (NPA) are lipid binding/transport molecules that elicit elevated levels of IgE response in the infected host, leading to Th2 type of immune response. They also transport arachidonic acid and its metabolites that are known to be involved in the action of antifilarial drug, Diethylcarbamazine and hence are of great significance for the control of lymphatic filariasis. We investigated the polymorphism of gp15/400 polyprotein of 35 isolates of lymphatic filarial parasite Wuchereria bancrofti collected from different geographic locations of India. The repeat sub-unit of the gene was found to be highly conserved in all the isolates with only two nucleotide synonymous changes at positions 286 (A-G) and 337 (C-T). Since this molecule is highly conserved and has multifarious roles in the survival and pathogenesis of the parasite it has good potential as a target for drug, immunodulation tool and immunotherapy development.

Allergens↗

Polymorphism of gp15/400 allergen gene of Wuchereria bancrofti from different regions of India endemic for lymphatic filariasis.

Nematode polyprotein allergens (NPA) are lipid-binding/transport molecules that elicit elevated levels of IgE response in the infected host, leading to Th2 type of immune response. They also transport arachidonic acid and metabolites that is known to be the action of antifilarial drug, diethylcarbamazine, and hence are of great significance to the control of lymphatic filariasis. We investigated the polymorphism of gp15/400 polyprotein of 35 isolates of lymphatic filarial parasite Wuchereria bancrofti collected from different geographic locations of India. The repeat subunit of the gene was found to be highly conserved in all the isolates with only two nucleotide synonymous changes at positions 369 (A-G) and 375 (C-T). As this molecule is highly conserved and has multifarious roles in the survival and pathogenesis of the parasite, it has good potential as a target for drug, immunodulation tools and immunotherapy development.

Allergens↗