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Accumulation of maize chlorotic dwarf virus proteins in its plant host and leafhopper vector.

The genome of Maize chlorotic dwarf virus (MCDV; genus Waikavirus; family Sequiviridae) consists of a monopartite positive-sense RNA genome encoding a single large polyprotein. Antibodies were produced to His-fusions of three undefined regions of the MCDV polyprotein: the N-terminus of the polyprotein (R78), a region between coat proteins (CPs) and the nucleotide-binding site (NBS) (R37), and a region between the NBS and a 3C-like protease (R69). The R78 antibodies react with proteins of 50 kDa (P50), 35 kDa (P35), and 25 kDa (P25) in virus preparations, and with P35 in plant extracts. In extracts of the leafhopper vector Graminella nigrifrons fed on MCDV-infected plants, the R78 antibodies reacted with P25 but not with P50 and P35. The R69 antibodies bound proteins of approximately 36 kDa (P36), 30 kDa (P30), and 26 kDa (P26) in virus preparations, and P36 and P26 in plant extracts. Antibodies to R37 reacted with a 26-kDa protein in purified virus preparations, but not in plant extracts. Neither the R69 nor the R37 antibodies bound any proteins in G. nigrifrons. Thus, in addition to the three CPs, cysteine protease and RNA-dependent RNA polymerase, the MCDV polyprotein is apparently post-transitionally cleaved into P50, P35, P25, P36, P30, and P26.

Amino Acid Sequence↗

The backbone conformational entropy of protein folding: experimental measures from atomic force microscopy.

The energy dissipated during the atomic force microscopy-based mechanical unfolding and extension of proteins is typically an order of magnitude greater than their folding free energy. The vast majority of the "excess" energy dissipated is thought to arise due to backbone conformational entropy losses as the solvated, random-coil unfolded state is stretched into an extended, low-entropy conformation. We have investigated this hypothesis in light of recent measurements of the energy dissipated during the mechanical unfolding of "polyproteins" comprised of multiple, homogeneous domains. Given the assumption that backbone conformational entropy losses account for the vast majority of the energy dissipated (an assumption supported by numerous lines of experimental evidence), we estimate that approximately 19(+/-2)J/(mol K residue) of entropy is lost during the extension of three mechanically stable beta-sheet polyproteins. If, as suggested by measured peak-to-peak extension distances, pulling proceeds to near completion, this estimate corresponds to the absolute backbone conformational entropy of the unfolded state. As such, it is exceedingly close to previous theoretical and semi-empirical estimates that place this value at approximately 20J/(mol K residue). The estimated backbone conformational entropy lost during the extension of two helical polyproteins, which, in contrast to the mechanically stable beta-sheet polyproteins, rupture at very low applied forces, is three- to sixfold less. Either previous estimates of the backbone conformational entropy are significantly in error, or the reduced mechanical strength of the helical proteins leads to the rupture of a subsequent domain before full extension (and thus complete entropy loss) is achieved.

Entropy↗

The structure of tobacco ringspot virus: a link in the evolution of icosahedral capsids in the picornavirus superfamily.

BACKGROUND: Tobacco ringspot virus (TRSV) is a member of the nepovirus genus of icosahedral RNA plant viruses that cause disease in fruit crops. Nepoviruses, comoviruses and picornaviruses are classified in the picornavirus superfamily. Crystal structures of comoviruses and picornaviruses and the molecular mass of the TRSV subunit (sufficient to accommodate three beta-barrel domains) suggested that nepoviruses may represent a link in the evolution of the picornavirus capsids from a T = 3 icosahedral virus. This evolutionary process is thought to involve triplication of the capsid protein gene, to encode a three-domain polyprotein, followed by development of cleavage sites in the interdomain linking regions. Structural studies on TRSV were initiated to determine if the TRSV subunit corresponds to the proposed uncleaved three-domain polyprotein. RESULTS: The 3.5 A resolution structure of TRSV shows that the capsid protein consists of three beta-barrel domains covalently linked by extended polypeptides. The order of connectivity of the domains in TRSV confirms the proposed connectivity for the precleaved comovirus and picornavirus capsid polyprotein. Structural differences between equivalent domains in TRSV and comoviruses are confined to the external surface loops, interdomain connecting polypeptides and N termini. The three different domains within TRSV and comoviruses are more closely related at the structural level than the three individual domains within picornaviruses. CONCLUSIONS: The structural results confirm the notion of divergent evolution of the capsid polyproteins of nepoviruses, comoviruses and picornaviruses from a common ancestor. A number of residues were found to be conserved among various nepoviruses, some of which stabilize the quaternary structure of the three domains in the TRSV capsid protein subunit. Two conserved regions were identified on the external surface of TRSV, however, mutational studies will be needed to understand their functional significance. Nepoviruses transmitted by the same nematode species do not share regions with similar amino acid composition on the viral surface.

Amino Acid Sequence↗

Abelson murine leukaemia virus transformation involves loss of epidermal growth factor-binding sites.

Malignant transformation by mammalian RNA sarcoma viruses has previously been shown to involve a reduction in receptor sites for a well characterized 6,000-molecular weight (MW) growth-promoting substance, designated epidermal growth factor (EGF). Although Abelson murine leukaemia virus (AbLV) resembles sarcoma viruses in its ability to transform embryo fibroblasts in cell culture, AbLV induces a rapid B-cell lymphoid leukaemia rather than fibrosarcomas in vivo. The major translational product of AbLV is a highly phosphorylated polyprotein of MW 120,000 which exhibits an associated tyrosine-specific protein kinase activity and probable transforming function. We show here that AbLV transformation resembles transformation by RNA sarcoma viruses with respect to the abolition of EGF-binding sites. EGF binding is restored to control levels following loss of polyprotein expression in morphological revertants of AbLV-transformed clones and remains uninfluenced in cell lines infected with transformation-defective (td) AbLV mutants encoding polyproteins deficient in protein kinase activity. These findings indicate that AbLV transformation involves a polyprotein-associated, tyrosine-specific protein kinase activity which mediates its effect through a mechanism resulting directly or indirectly in the abolition of EGF-binding sites.

Abelson murine leukemia virus↗

Structure of the catalytic domain of the hepatitis C virus NS2-3 protease.

Hepatitis C virus is a major global health problem affecting an estimated 170 million people worldwide. Chronic infection is common and can lead to cirrhosis and liver cancer. There is no vaccine available and current therapies have met with limited success. The viral RNA genome encodes a polyprotein that includes two proteases essential for virus replication. The NS2-3 protease mediates a single cleavage at the NS2/NS3 junction, whereas the NS3-4A protease cleaves at four downstream sites in the polyprotein. NS3-4A is characterized as a serine protease with a chymotrypsin-like fold, but the enzymatic mechanism of the NS2-3 protease remains unresolved. Here we report the crystal structure of the catalytic domain of the NS2-3 protease at 2.3 A resolution. The structure reveals a dimeric cysteine protease with two composite active sites. For each active site, the catalytic histidine and glutamate residues are contributed by one monomer, and the nucleophilic cysteine by the other. The carboxy-terminal residues remain coordinated in the two active sites, predicting an inactive post-cleavage form. Proteolysis through formation of a composite active site occurs in the context of the viral polyprotein expressed in mammalian cells. These features offer unexpected insights into polyprotein processing by hepatitis C virus and new opportunities for antiviral drug design.

Animals↗

Probing the substrate specificity of the dengue virus type 2 NS3 serine protease by using internally quenched fluorescent peptides.

The NS3 (dengue virus non-structural protein 3) serine protease of dengue virus is an essential component for virus maturation, thus representing an attractive target for the development of antiviral drugs directed at the inhibition of polyprotein processing. In the present study, we have investigated determinants of substrate specificity of the dengue virus NS3 protease by using internally quenched fluorogenic peptides containing Abz (o-aminobenzoic acid; synonymous to anthranilic acid) and 3-nitrotyrosine (nY) representing both native and chimaeric polyprotein cleavage site sequences. By using this combinatorial approach, we were able to describe the substrate preferences and determinants of specificity for the dengue virus NS2B(H)-NS3pro protease. Kinetic parameters (kcat/K(m)) for the hydrolysis of peptide substrates with systematic truncations at the prime and non-prime side revealed a length preference for peptides spanning the P4-P3' residues, and the peptide Abz-RRRRSAGnY-amide based on the dengue virus capsid protein processing site was discovered as a novel and efficient substrate of the NS3 protease (kcat/K(m)=11087 M(-1) x s(-1)). Thus, while having confirmed the exclusive preference of the NS3 protease for basic residues at the P1 and P2 positions, we have also shown that the presence of basic amino acids at the P3 and P4 positions is a major specificity-determining feature of the dengue virus NS3 protease. Investigation of the substrate peptide Abz-KKQRAGVLnY-amide based on the NS2B/NS3 polyprotein cleavage site demonstrated an unexpected high degree of cleavage efficiency. Chimaeric peptides with combinations of prime and non-prime sequences spanning the P4-P4' positions of all five native polyprotein cleavage sites revealed a preponderant effect of non-prime side residues on the K(m) values, whereas variations at the prime side sequences had higher impact on kcat.

Dengue Virus↗

A Ty3/gypsy retrotransposon-like sequence localizes to the centromeric regions of cereal chromosomes.

A 745 bp sequence (pSau3A9) located at the centromeres of several cereal species was isolated from a sorghum BAC library by Jiang et al. (1996, Proc. Natl Acad. Sci. USA, 93, 14210-14213). We have amplified a partially homologous 809 bp sequence from barely genomic DNA by PCR and localized it to the centromeres of barley, wheat and rye chromosomes by fluorescent in situ hybridization (FISH). Sequence analysis showed this barley homolog of pSau3A9 to have high similarity to the integrase region of the polyprotein gene of Ty3/gypsy group retrotransposons. Using this integrase sequence as a probe, several clones were isolated from a lambda library constructed of genomic barley DNA. One of the lambda clones contained coding regions for all five catalytic sites characteristic of the retrotransposon polyprotein. Two direct repeats flanking the polyprotein gene are homologous to the cereal centromeric sequence described by Aragón-Alcaide et al. (1996, Chromosoma, 105, 261-268) and may represent all or part of the long-terminal repeats (LTRs). Different plasmid subclones containing various regions of the lambda clone were used in FISH to show that the entire polyprotein gene and upstream flanking sequences, including the presumed LTR, are present at barley centromeres. The preferential (or exclusive) localization of an apparently complete retroelement within the centromeric regions of several cereal species raises interesting questions about its role in karyotype evolution and centromere function.

Amino Acid Sequence↗

Complete translation of poliovirus RNA in a eukaryotic cell-free system.

Poliovirus RNA stimulates imcorporation of 35S from both [35S]methionine and formyl-[35S]methionyl-tRNAfMet in cell-free systems derived from HeLa cells or from poliovirus-infected HeLa cells. The largest product formed under the direction of the viral RNA is the same size as the polyprotein thought to represent translation of the entire RNA. Synthesis of this polyprotein and other large products was stimulated greatly by increasing the salt concentration during the reaction from the optimum for initiation (90 mM) to the optimum for elongation (155 mM). Only one initiation peptide could be identified, and a tryptic digest of the product contained mainly peptides that cochromatographed with peptides from authentic viral proteins. The RNA from a deletion mutant of poliovirus initiated protein synthesis at the same site used by standard RNA and programmed synthesis of an appropriately deleted set of polypeptides. The results strongly support the model of translation of poliovirus RNA from a single initiation site into a continuous polyprotein that is cleaved to form the functional proteins. It is suggested that uninfected HeLa cell extracts can carry out the cleavages of nascent polyprotein.

Cell-Free System↗

Evidence for three classes of avian sarcoma viruses: comparison of the transformation-specific proteins of PRCII, Y73, and Fujinami viruses.

The gag-linked transformation-specific proteins (polyproteins( of PRCII, Fujinami, and Y73 avian sarcoma viruses have been compared by tryptic peptide mapping. In addition to shared gag peptides, PRCII polyprotein p105 and FSV polyprotein p140 were found to have seven methionine-containing and five cysteine-containing tryptic peptides in common. These represent the majority of the non-gag peptides for each virus. In contrast, no overlap was detected with the non-gag peptides of the Y73 polyprotein p90. Examination of the tryptic phosphopeptides of p105, p140, and p90 labeled by their associated protein kinases gave similar results. Although the major phosphopeptides of p105 and p140 comigrated, they were distinct from the phosphopeptide of p90. Three classes of transformation-specific proteins can now be identified among known avian sarcoma viruses. After the pp60src of Rous sarcoma virus and B77 virus, the proteins of PRCII and Fujinami virus form a second class and Y73--currently the only representative--characterizes the third. Despite their structural differences, these viruses may share a common mechanism of transformation, effected by their associated protein kinases.

Alpharetrovirus↗

A third class of avian sarcoma viruses, defined by related transformation-specific proteins of Yamaguchi 73 and Esh sarcoma viruses.

The gag-linked transformation-specific protein (polyprotein) p80 of Esh avian sarcoma virus (ESV) has been compared by tryptic peptide mapping with the homologous protein p90 of Yamaguchi 73 avian sarcoma virus (Y73). p80 of ESV and p90 of Y73 were found to share all four of their major nonstructural, transformation-specific, methionine-containing peptides and to have at least seven cysteine-containing transformation-specific peptides in common. Two nonstructural cysteine-containing peptides unique for ESV p80 and three specific for Y73 p90 were also identified. None of these peptides were found in the transforming gene product pp60src of Rous sarcoma virus (RSV) or in the transformation-specific polyproteins p105 of avian sarcoma virus PRCII (PRCII) or p140 of Fujinami sarcoma virus (FSV). ESV p80 and Y73 p90 are phosphorylated, and their tryptic phosphopeptides appear to be identical. In each polyprotein two major phosphopeptides were demonstrated, one containing phosphoserine, the other phosphotyrosine. The latter serves as phosphoacceptor for the protein kinase activities (ATP:protein phosphotransferase, EC 2.7.1.37) associated with p80 and p90. These protein kinase activities were found to be functionally indistinguishable but could be easily distinguished from the activities associated with PRCII p105 and FSV p140 on the basis of their cation requirement and target site specificity. On that basis also, p80/p90-associated protein kinases were found to be more similar to the enzymatic activity of pp60src than to those associated with the PRCII and FSV transformation-specific polyproteins. These results document a close genetic relationship between the two independently isolated sarcoma viruses Y73 and ESV. On the basis of the relatedness of transformation-specific proteins, ESV and Y73 constitute class III of avian sarcoma viruses, with class I containing the various strains of RSV and class II encompassing FSV and PRCII.

Alpharetrovirus↗

The hepatitis C virus NS3 serine proteinase and NS4A cofactor: establishment of a cell-free trans-processing assay.

The hepatitis C virus RNA genome encodes a long polyprotein that is proteolytically processed into at least 10 products. The order of these cleavage products in the polyprotein is NH2-C-E1-E2-p7-NS2-NS3-NS4A-NS4B-NS5A-NS5B -COOH. A serine proteinase domain located in the N-terminal one-third of nonstructural protein NS3 mediates cleavage at four downstream sites (the 3/4A, 4A/4B, 4B/5A, and 5A/5B sites). In addition to the proteinase catalytic domain, the NS4A protein is required for processing at the 4B/5A site but not at the 5A/5B site. These cleavage events are likely to be essential for virus replication, making the serine proteinase an attractive antiviral target. Here we describe an in vitro assay where the NS3-4A polyprotein, NS3, the serine proteinase domain (the N-terminal 181 residues of NS3), and the NS4A cofactor were produced by cell-free translation and tested for trans-processing of radiolabeled substrates. Polyprotein substrates, NS4A-4B or truncated NS5A-5B, were cleaved in trans by all forms of the proteinase, whereas NS4A was also required for NS4B-5A processing. Proteolysis was abolished by substitution mutations previously shown to inactivate the proteinase or block cleavage at specific sites in vivo. Furthermore, N-terminal sequence analysis established that cleavage in vitro occurred at the authentic 4A/4B site. Translation in the presence of microsomal membranes enhanced processing for some, but not all, proteinase-substrate combinations. Trans-processing was both time and temperature dependent and was eliminated by treatment with a variety of detergents above their critical micelle concentrations. Among many common proteinase inhibitors tested, only high (millimolar) concentrations of serine proteinase inhibitors tosyllysyl chloromethyl ketone and 4-(2-aminoethyl)benzenesulfonyl fluoride inactivated the NS3 proteinase. This in vitro assay should facilitate purification and further characterization of the viral serine proteinase and identification of molecules which selectively inhibit its activity.

Animals↗

"Natively unfolded" VPg is essential for Sesbania mosaic virus serine protease activity.

Polyprotein processing is a major strategy used by many plant and animal viruses to maximize the number of protein products obtainable from a single open reading frame. In Sesbania mosaic virus, open reading frame-2 codes for a polyprotein that is cleaved into different functional proteins in cis by the N-terminal serine protease domain. The soluble protease domain lacking 70-amino-acid residues from the N terminus (deltaN70Pro, where Pro is protease) was not active in trans. Interestingly, the protease domain exhibited trans-catalytic activity when VPg (viral protein genome-linked) was present at the C terminus. Bioinformatic analysis of VPg primary structure suggested that it could be a disordered protein. Biophysical studies validated this observation, and VPg resembled "natively unfolded" proteins. CD spectral analysis showed that the deltaN70Pro-VPg fusion protein had a characteristic secondary structure with a 230 nm positive CD peak. Mutation of Trp-43 in the VPg domain to phenylalanine abrogated the positive peak with concomitant loss in cis- and trans-proteolytic activity of the deltaN70Pro domain. Further, deletion of VPg domain from the polyprotein completely abolished proteolytic processing. The results suggested a novel mechanism of activation of the protease, wherein the interaction between the natively unfolded VPg and the protease domains via aromatic amino acid residues alters the conformation of the individual domains and the active site of the protease. Thus, VPg is an activator of protease in Sesbania mosaic virus, and probably by this mechanism, the polyprotein processing could be regulated in planta.

Amino Acid Sequence↗

Recognition and analysis of protein-coding genes in severe acute respiratory syndrome associated coronavirus.

MOTIVATION: The recent outbreak of severe acute respiratory syndrome (SARS) caused by SARS coronavirus (SARS-CoV) has necessitated an in-depth molecular understanding of the virus to identify new drug targets. The availability of complete genome sequence of several strains of SARS virus provides the possibility of identification of protein-coding genes and defining their functions. Computational approach to identify protein-coding genes and their putative functions will help in designing experimental protocols. RESULTS: In this paper, a novel analysis of SARS genome using gene prediction method GeneDecipher developed in our laboratory has been presented. Each of the 18 newly sequenced SARS-CoV genomes has been analyzed using GeneDecipher. In addition to polyprotein 1ab(1), polyprotein 1a and the four genes coding for major structural proteins spike (S), small envelope (E), membrane (M) and nucleocapsid (N), six to eight additional proteins have been predicted depending upon the strain analyzed. Their lengths range between 61 and 274 amino acids. Our method also suggests that polyprotein 1ab, polyprotein 1a, S, M and N are proteins of viral origin and others are of prokaryotic. Putative functions of all predicted protein-coding genes have been suggested using conserved peptides present in their open reading frames. AVAILABILITY: Detailed results of GeneDecipher analysis of all the 18 strains of SARS-CoV genomes are available at http://www.igib.res.in/sarsanalysis.html

Algorithms↗

Nucleotide sequence of Hungarian grapevine chrome mosaic nepovirus RNA1.

The nucleotide sequence of the RNA1 of hungarian grapevine chrome mosaic virus, a nepovirus very closely related to tomato black ring virus, has been determined from cDNA clones. It is 7212 nucleotides in length excluding the 3' terminal poly(A) tail and contains a large open reading frame extending from nucleotides 216 to 6971. The presumably encoded polyprotein is 2252 amino acids in length with a molecular weight of 250 kDa. The primary structure of the polyprotein was compared with that of other viral polyproteins, revealing the same general genetic organization as that of other picorna-like viruses (comoviruses, potyviruses and picornaviruses), except that an additional protein is suspected to occupy the N-terminus of the polyprotein.

Amino Acid Sequence↗

The complete nucleotide sequence of coxsackievirus B4 and its comparison to other members of the Picornaviridae.

The genome of the prototype stain of coxsackievirus B4 (J.V.B. Benschoten) has been cloned in Escherichia coli and its complete nucleotide sequence determined. Excluding the poly(A) tract, the RNA genome is 7395 nucleotides in length and appears to encode a single polyprotein of 2183 amino acids. The predicted amino acid sequence of the polyprotein shows close homology (88%) to that of the previously sequenced coxsackievirus B3 and to certain regions of the polyproteins of the polioviruses and human rhinovirus 14. This allows identification of putative polyprotein cleavage signals, antigenic domains and other structural features likely to be important to the biological integrity of the virus.

Amino Acid Sequence↗

Translocation and cleavage of rubella virus envelope glycoproteins: identification and role of the E2 signal sequence.

The structural proteins of rubella virus (RV) are translated as a large polyprotein precursor, p110, which is processed to produce the mature virion components, the 33K capsid protein (C) and the two envelope glycoproteins, E1 (58K) and E2 (42K to 47K). The precise processing mechanism has not been elucidated; however it must include at least two proteolytic cleavages to release the individual virion components from the polyprotein, and it must provide for their dichotomous intracellular distribution. The C protein remains in the cytoplasm where it participates in the formation of nucleocapsids, while the envelope glycoproteins enter the cellular secretory pathway and are N-glycosylated and cleaved. Sequence analysis of the 24S mRNA encoding the polyprotein precursor suggests that both E1 and E2 are preceded by signal peptides for translocation across the membrane of the rough endoplasmic reticulum. A recent study has provided direct evidence that the putative signal peptide preceding E1 can in fact mediate translocation of E1. In this study, we have used in vitro translation-translocation assays to examine further the processing of RV glycoproteins. We have shown that the putative signal sequence preceding E2 can mediate translocation of the E2 protein in the absence of an intact E1 signal peptide. The experiments also revealed that cleavage of the E2-E1 polyprotein requires (i) the E2 signal peptide, (ii) microsomal membranes and (iii) sequences beyond the proximal half of the E1 signal peptide. Together these results suggest that separation of the E2 signal sequence as well as the proteolytic cleavage of E1 from E2 is performed by the cellular enzyme, signal peptidase.

Amino Acid Sequence↗

Virus-specific proteins in cells infected with tomato black ring nepovirus: evidence for proteolytic processing in vivo.

The synthesis of proteins encoded by the RNA of tomato black ring virus (TBRV) in vivo was studied in protoplasts by direct labelling with [35S]methionine, and in protoplasts and plants by immunoblotting experiments with specific antisera. Comparison of the proteins synthesized in infected and mock-inoculated protoplasts suggested that proteins of M(r) 120K, 90K, 80K, 57K and 46K were virus-specific. The proteins derived from the RNA-1-encoded polyprotein detected by immunoblotting were a stable 120K protein and, only in protoplasts, small amounts of a 90K protein which contains the C-terminal part of the 120K protein and the polymerase domain. The results suggest that the polymerase and the adjacent protease function in vivo largely or solely when combined in a 120K protein. The proteins derived from the RNA-2-encoded polyprotein detected by immunoblotting were 59K and 57K proteins, which reacted with antiserum to TBRV particles, and a 46K protein. In extracts of infected Nicotiana clevelandii and Chenopodium quinoa made soon after inoculation, the 59K protein was more abundant than the 57K protein; later samples contained similar quantities of each protein. The 57K protein comigrated with protein extracted from virus particles. The results of amino acid sequencing suggested that the 57K protein is derived from the 59K protein by the loss of nine C-terminal amino acids. Antiserum to a peptide adjacent to the 57K protein in the 150K polyprotein detected a 46K protein in protoplasts and plant tissue. The results support the processing scheme for TBRV polyproteins proposed after analysis of the products of in vitro translation.

Amino Acid Sequence↗

Expression of potyvirus proteins in insect cells infected with a recombinant baculovirus.

The N-terminal portion (P1-HC-Pro-P3) of the tobacco vein mottling virus (TVMV) polyprotein was expressed in insect cells and larvae by a recombinant baculovirus. The proteases necessary to process this TVMV polyprotein fragment were active in insect cells, since mature P1, HC-Pro and P3 proteins were detected by specific antisera in Western blots. Antisera to P1, HC-Pro and P3 also recognized polypeptides with apparent M(r) values predicted for the intermediate processing products of the polyprotein fragment. The results of this study indicate that the autocatalytic processing of TVMV HC-Pro from the polyprotein is supported by insect cells. Helper component activity in extracts of cells infected with recombinant baculovirus was not detected by aphid transmission assay.

Animals↗