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PubMed1998

Proteolytic mapping of the coronavirus infectious bronchitis virus 1b polyprotein: evidence for the presence of four cleavage sites of the 3C-like proteinase and identification of two novel cleavage products.

We have previously reported that the 3C-like proteinase of the coronavirus infectious bronchitis virus (IBV) is responsible for processing of the 1a and 1a/1b polyproteins to three mature products of 24, 10, and 100 kDa (Liu et al., 1994, 1997; Ng and Liu, 1998). The C-terminal cleavage site of the 100-kDa protein was defined to be the Q891(1b)-S892(1b) dipeptide bond encoded by nucleotides 15,129 to 15,134 (Liu and Brown, 1995). In this report, other cleavage sites of the 3C-like proteinase in the polyprotein encoded by the ORF 1b region were mapped by coexpression, deletion, and site-directed mutagenesis studies. Using two ORF 1b-specific antisera, V58 and V17, three more Q-S(G) dipeptide bonds, encoded by nucleotides 16,929 to 16,934, 18,492 to 18,497, and 19,506 to 19,511, respectively, were demonstrated to be the cleavage sites of the 3C-like proteinase. Cleavage at these four positions would result in the release of four mature products with molecular masses of approximately 68, 58, 39, and 35 kDa. Among them, the 39- and 35-kDa proteins were specifically identified in IBV-infected cells. Taken together with the 100-kDa protein previously identified, these results suggest that the ORF 1b region of IBV mRNA1 may be able to encode five mature products.

Animals↗

PubMed1999

Antigenic epitopes of the hepatitis A virus polyprotein.

Forty-two antigenic domains were identified across the hepatitis A virus (HAV) polyprotein by using a set of 237 overlapping 20-mer synthetic peptides spanning the entire HAV polyprotein and a panel of serum samples from acutely HAV-infected patients. The term "antigenic domain" is used in this study to define a protein region spanned with consecutive overlapping immunoreactive peptides. Nineteen antigenic domains were found within the structural proteins, and 22 were found within the nonstructural proteins, with 1 domain spanning the junction of VP1 and P2A proteins. Five of these domains were considered immunodominant, as judged by both the breadth and the strength of their immunoreactivity. One domain is located within the VP2 protein at position 57-90 aa. A second domain, located at position 767-842 aa, contains the C-terminal part of the VP1 protein and the entire P2A protein. A third domain, located at position 1403-1456 aa, comprises the C-terminal part of the P2C protein and the N-terminal half of the P3A protein. The fourth domain, located at position 1500-1519 aa, includes almost the entire P3B, and the last domain, located at position 1719-1764 aa, contains the C-terminal region of the P3C protein and the N-terminal region of the P3D protein. It is interesting to note that four of the five most immunoreactive domains are derived from small HAV proteins and/or encompass protein cleavage sites separating different HAV proteins. The HAV-specific immunoreactivity of each antigenically reactive peptide was confirmed by using seven HAV seroconversion panels. Collectively, these data demonstrate that HAV structural and nonstructural proteins contain antigenic epitopes that can be efficiently modeled with short synthetic peptides.

Amino Acid Sequence↗

PubMed1994

Alphavirus positive and negative strand RNA synthesis and the role of polyproteins in formation of viral replication complexes.

The genome of alphaviruses is translated into polyproteins that are processed into a viral replicase that produces both negative and positive strands. In infected cells, negative strand synthesis is short-lived and occurs only early, whereas positive strand synthesis is stable and occurs both early and late. Analysis of temperature sensitive mutants indicated: nsP1 functioned in the initiation of transcription; nsP3 acted to form initial transcription complexes; and nsP2 and nsP4 first recognized positive strands as templates and then made negative strands the preferred templates. While nsP4 and nsP1 individually rescued early defects in transcription, nsP2 and nsP3 acted initially in cis. We interpret our results to suggest nsP1234 was cleaved to nsP4, nsP1 and nsP23, bound a positive strand and synthesized a negative strand. Cleavage of P23 or other modifications to nsP2 and nsP4 convert the initial transcription complex to a stable complex that synthesizes positive strands. Negative strand synthesis is unstable because of the failure to form initial transcription complexes after host factors that are part of the replicase are depleted or the half-life of polyprotein precursors like P23 is shortened.

Alphavirus↗

PubMed1993

Precursor of the nuclear-encoded extrinsic 30 kDa protein in photosystem II of Euglena gracilis Z is not a polyprotein.

Polyprotein-type precursors have been reported for the nuclear-encoded proteins such as the small subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) and the apoproteins of light-harvesting chlorophyll-protein (LHC) in Euglena. We report here that the precursor of the extrinsic 30 kDa protein of photosystem II (PS II) encoded by nuclear DNA is not a polyprotein. The precursor was identified as a 45 kDa protein by immunoprecipitation of in vitro translation products of mRNA and by a pulse-chase experiment. It is probable that the structure of the precursor of the nuclear-encoded protein in Euglena chloroplast is closely related to the feature of assembly, as well as of transport, of the protein in chloroplast.

Animals↗

PubMed1990

Study of the gag-coded polyproteins of type D retroviruses. Block of glycosylation inhibits the processing of major structural protein.

The study of the gag-coded glycosylated polyprotein (gPr78gag) from type D retrovirus-producing cells is reported. It is shown that glycosylation inhibitors tunicamycin and 2-deoxy-D-glucose are blocking the synthesis of gPr78gag. This demonstrates that gPr78gag is a N-glycan. The protein part of gPr78gag is supposedly identified (MW = 65 k). The inhibitors used partially stopped the processing of gag-coded polyprotein Pr78gag into core protein p27 as shown in pulse-chase experiments.

Deoxyglucose↗

PubMed1994

Detection of a 45 kD protein derived from the N terminus of the pea seedborne mosaic potyvirus polyprotein in vivo and in vitro.

A 45 kD protein (Pro1) derived from the N terminus of the pea seedborne mosaic potyvirus (PSbMV) polyprotein has been detected in extracts of infected pea plants and among in vitro translation products of PSbMV genomic RNA. The genomic region coding for the first 231 amino acids of the PSbMV polyprotein was cloned and expressed in Escherichia coli as a fusion protein with beta-galactosidase. A rabbit antiserum raised against the fusion protein recognized an approximately 45 kD protein in immunoblots of extracts of PSbMV-infected pea leaves that was not present in extracts of healthy leaves. The highest concentration of the 45 kD protein was found in extracts of young leaves, suggesting the protein may be rapidly degraded in vivo. After in vitro translation of PSbMV genomic RNA in a wheat germ extract, the antiserum immunoprecipitated a 45 kD polypeptide as well as some lower molecular weight translation products. On the other hand, an approximately 90 kD polypeptide was immunoprecipitated from in vitro translation products of genomic RNA in a rabbit reticulocyte lysate, corresponding to the combined molecular weights of Pro1 and the helper component predicted from genomic sequence data.

Binding Sites↗

PubMed1984

Partial N-terminal amino acid sequences of polypeptides p14 and p12 of encephalomyocarditis virus are identical and correspond to the N-terminus of the viral polyprotein.

Our previous data suggested that translation in an EMC virus RNA-programmed cell-free system from Krebs-2 cells is initiated predominantly at a single site and that the earliest amino acid sequences synthesized correspond to non-structural 'leader' polypeptides p14 and p12 [(1982) FEBS Lett. 141, 153-156]. Here, polypeptides p14 and p12 were labelled in vitro by tritiated amino acids, isolated and subjected to automated Edman degradation. Both polypeptides (after the loss of the N-terminal methionine) were shown to contain alanine in position 1 and glutamic acid in positions 5 and 7. These and other data demonstrate that p14 and p12 share a common N-terminal sequence. This sequence coincides precisely with the N-terminus of EMC virus polyprotein sequence deduced from the primary structure of the viral genome [(1984) Nucleic Acids Res., in press]. Thus, the single initiation site operating in our translation system corresponds to the start of the polyprotein molecule.

Amino Acid Sequence↗

PubMed1991

Mutating P2 and P1 residues at cleavage junctions in the HIV-1 pol polyprotein. Effects on hydrolysis by HIV-1 proteinase.

Mutations were introduced into the P2 and P1 positions of the junctions, (a) linking reverse transcriptase (RT) and integrase (IN) (-Leu*Phe-) and (b) between the p51 and RNase H domain (-Phe*Tyr-) within p66 of RT in the HIV-1 pol polyprotein. Processing by HIV proteinase (PR) in cis was monitored upon expression of these constructs in E. coli. Whereas the presence of Leu or Phe in P1 permitted rapid cleavage at either junction, substitution of a beta-branched (Ile) hydrophobic residue essentially abolished hydrolysis. By contrast, placement of a beta-branched (Val) residue in the P2 position flanking such -Hydrophobic*Hydrophobic- junctions resulted in effective cleavage of the scissile peptide bond. Gly in P2, however, abrogated cleavage. The significance of these findings in terms of PR specificity, polyprotein processing and the generation of homodimeric (p51/p51) RT for crystallisation purposes is discussed.

Base Sequence↗

PubMed1992

Prokaryotic polyprotein precursors.

Polyproteins have been found only recently in prokaryotes. The four known examples of single bacterial genes encoding precursors that are posttranslationally processed into two mature proteins are addressed here with respect to (i) their genomic arrangement, (ii) the sites of proteolytic processing, (iii) the relevant proteases, (iv) their maturation pathway, and (v) the function of the mature proteins. How these polyproteins may have evolved is also discussed.

Bacteria↗

PubMed1996

Extended binding sites of cyclophilin as revealed by the interaction with HIV-1 Gag polyprotein derived oligopeptides.

Oligopeptides derived from the gag polyprotein (Pr55gag) of human immunodeficiency virus type 1 (HIV-1) segment were used to evaluate the extension of the putative binding region for the complex of Pr55gag and the human cytosolic peptidyl prolyl cis/trans isomerase (PPIase) 18 kDa cyclophilin (Cyp18). Five N-terminally acetylated, C-terminally amidated oligopeptides containing one (HIV-1 Gag218-224; 1), two (HIV-1 Gag218-226 and HIV-1 Gag217-224; 2 and 3, respectively), three (HIV-1 Gag217-226; 4) or four (HIV-1 Gag213-237; 5) proline residues were synthesized. Using competition experiments with a standard substrate the binding affinities to Cypl8 of the synthesized peptides were determined. The IC50 value of 184 microM for the 25-mer peptide 5 was fivefold or more lower than those of the peptides 1-4 lacking one or more prolines. Failure of competition in assays containing enzymes of other PPIase families by millimolar concentrations of 5 revealed a Cyp18 specific interaction involving the active site of the enzyme. In its far UV circular dichroism, aqueous solutions of 5 display properties of random coil conformation, but spectra were also consistent with a small contribution of proline specific secondary structures. However, a proline-rich peptide typical of forming left-handed polyproline II helices did not compete for the active site of Cypl8. The results demonstrate that the putative binding region of HIV-1 gag polyprotein has a certain degree of binding affinity to the PPIase site of Cyp18, and may add a previously unrecognized topological component to the known subsite specificity of cyclophilins.

Amino Acid Isomerases↗

PubMed1983

Gag-mos Polyproteins encoded by variants of the Moloney strain of mouse sarcoma virus.

Two revertants of ts110 Moloney murine sarcoma virus (MuSV) with wild-type MuSV phenotype were examined for the presence of mos gene products, ts110 MuSV has a temperature-sensitive defect in a function required to maintain the transformed phenotype. The nonproducer 6m2 cell clone transformed by ts110 produces an 85,000-Da gag-mos protein (P85gag-mos) and a 58,000-Da gag protein (P58gag). A spontaneous revertant (clone 54-5A4) of the 6m2 cell clone produces a 100,000-Da protein (P100) recognized by antisera raised against murine leukemia virus p15, p12, and p30 but lacks determinants of p10, reverse transcriptase, and gp70. P100 was specifically recognized by antisera (anti-C3) prepared against a synthetic peptide representing the predicted C-terminal 12 amino acids of Moloney MuSV v-mos gene. Normal sera or anti-C3 blocked with excess synthetic peptide did not recognize P100. Thus, P100 is a product of the gag and mos genes. P100 was found to be phosphorylated. A second wild-type revertant (clone 204-3) was obtained by superinfection of ts110 nonproducer cells with Simian sarcoma associated virus (SSAV); it was also found to contain a phosphorylated P100gag-mos protein. The 204-3 cell clone also contained two gag polyproteins (Pr60gag and Pr55gag) of the size and antigenic properties of those found in SSAV-infected cells. These results provide two examples of P100 gag-mos proteins both derived from the P85gag-mos producing 6m2 cell clone. The P100 gag-mos polyproteins are made in amounts that are easily detected by radiolabeling experiments using [3H]leucine. The intracellular viral RNAs present in 6m2 cells and the two revertant clones were also examined. All three cell clones contained a 4.0 kb RNA hybridizing to v-mos sequences but only the 6m2 clone contained a 3.5 kb mos-containing RNA. Our findings indicate that the 3.5 kb RNA codes for P85gag-mos in cell-free translation experiments (Junghans et al., 1982, J. Mol. Biol. 161, 229). These findings as they relate to the mechanism that produces P100gag-mos instead of P85gag-mos are discussed.

Animals↗

PubMed1986

Inhibition of cleavage of Moloney murine leukemia virus gag and env coded precursor polyproteins by cerulenin.

Cerulenin, an inhibitor of de novo fatty acid (and cholesterol) biosynthesis, has been shown to significantly decrease (greater than 75%) the amount of Moloney murine leukemia virus (MMuLV) released into the culture medium of chronically infected mouse fibroblasts (I. Katoh, Y. Yoshinaka, and R.B. Luftig, 1986, Virus Res., in press). In order to clarify the mechanism by which this decrease in virus production occurs, we analyzed the kinetics of gag and env coded protein synthesis in M-MuLV infected, cerulenin-treated cells by immunoprecipitation with monospecific antisera to p30, p12, p10, gp70, and p15(E). We found that in pulse (15 min-2 hr)-chase (0-4 hr) experiments the cleavage of not only Pr65gag to p30 and other gag coded proteins but Pr80env to gp70 and Pr15(E) as well, was greatly reduced by cerulenin treatment. Further, since the total amount of label in the Pr65gag and Pr80env bands remained about the same or was slightly decreased in 2-hr pulsed, cerulenin-treated cells, this suggests that cerulenin decreases virus production, in part, by inhibiting the cleavage of both precursor gag and env coded polyproteins during virus assembly and budding at the cell membrane. We also observed that at longer chase periods (4 hr), the effect of cerulenin could be partially overriden in that minor amounts of cleaved gag and env coded polyproteins were produced and assembled into virion particles. However, these particles contained abnormally large amounts of the uncleaved precursor Pr65gag, suggesting that maturation was incomplete. The above results suggest two independent, but not exclusive, possible mechanisms of cerulenin action to block M-MuLV production, viz. cerulenin decreases the pool of fatty acids, thereby inhibiting fatty acid acylation of Pr65gag, as well as Pr80env, and thus preventing the interaction between gag (the p15 antigenic determinant on Pr65gag) and env [the p15(E) antigenic determinant of Pr15(E)] coded gene products at the cell membrane needed for efficient virus assembly (M. Satake and R. B. Luftig, 1983, Virology 124, 259-273), and cerulenin inhibits one or more proteolytic enzymes responsible for the cleavage of Pr65gag and Pr80env.

Antifungal Agents↗

PubMed1989

Inhibition of proteolytic processing of the polyproteins of cowpea mosaic virus by hemin.

Cleavages of the polyproteins synthesized from cowpea mosaic virus (CPMV) B RNA and M RNA in rabbit reticulocyte lysates are inhibited by hemin. Cleavage of the CPMV B RNA-encoded 200K polyprotein and of the M RNA-encoded 60K intermediary precursor protein were most sensitive to hemin inhibition, while cleavages of other precursor proteins were less sensitive. A significant observation was that at a hemin concentration of 25 microM, but not at higher concentrations, the 60K protein was cleaved to yield the two viral capsid proteins. This cleavage reaction has not been observed in vitro previously.

Electrophoresis, Polyacrylamide Gel↗

PubMed1990

Cleavage between nsP1 and nsP2 initiates the processing pathway of Sindbis virus nonstructural polyprotein P123.

The cleavage between nsP1 and nsP2 and that between nsP2 and nsP3 in the Sindbis virus nonstructural polyproteins was studied with respect to order of processing and enzyme-substrate relationships, using site-specific mutants in which the cleavage sites had been altered. The penultimate Gly in nsP1 or nsP2 or both was substituted by Ala, Val, or Glu, and processing was studied in vitro. Substitution with Ala resulted in partial cleavage whereas substitution with Val or Glu totally abolished cleavage at the mutagenized site. Abolishment of cleavage at the nsP2/nsP3 site did not affect processing at the nsP1/nsP2 site in the precursor polyprotein P123, and nsP1 and P23 were produced. When cleavage at the nsP1/nsP2 site was abolished, however, processing at the nsP2/nsP3 site was also prevented and P123 accumulated. To investigate why cleavage at the nsP1/nsP2 site should be required for cleavage at the nsP2/nsP3 site, the mutagenized polypeptides were used as enzymes in trans-cleavage experiments. We found that P123 can cleave the nsP1/nsP2 site but not the nsP2/nsP3 site, whereas P23 can cleave the nsP2/nsP3 site very efficiently. Thus, cleavage at the nsP1/nsP2 site by P123 is required to produce an enzyme capable of cleaving the nsP2/nsP3 site. Release of nsP4 from P1234 appears to be independent of the other cleavages and occurs primarily immediately after translation. These mutations were also transferred into a full-length cDNA clone of Sindbis virus and virus was recovered. Mutants defective in the cleavage of the nsP2/nsP3 site were temperature sensitive, growing at a slightly reduced rate compared to wild-type virus at 30 degrees but growing poorly at 40 degrees. Mutants defective in the cleavage of both the nsP1/nsP2 site and the nsP2/nsP3 site were viable but grew poorly compared with wild-type at any temperature.

Amino Acid Sequence↗

PubMed1986

A second virus-encoded proteinase involved in proteolytic processing of poliovirus polyprotein.

The poliovirus polyprotein is cleaved at three different amino acid pairs. Viral polypeptide 3C is responsible for processing at the most common pair (glutamineglycine). We have found that a cDNA fragment encoding parts of the capsid protein region (P1) and the nonstructural protein region (P2), and including the P1-P2 processing site (tyrosine-glycine), can be expressed in E. coli. The translation product was correctly processed. Disruption of the coding sequence of 2A, a nonstructural polypeptide mapping carboxy-terminal to the tyrosine-glycine cleavage site, by linker mutagenesis or deletion, prevented processing. Deletion of the adjacent polypeptide 2B had no such effect. Antibodies against 2A specifically inhibited processing at the 3C'-3D' processing site (tyrosine-glycine) in vitro. We conclude that poliovirus encodes the second proteinase 2A, which processes the polyprotein at tyrosine-glycine cleavage sites.

Capsid↗

PubMed1989

Distinct modes of poliovirus polyprotein initiation in vitro.

RNAs of poliovirus type 1 and type 3 were translated in extracts from Krebs-2 cells after annealing with oligodeoxyribonucleotides complementary to different sites in the 5'-untranslated region (5'-UTR). Due to a high level of endogenous RNase H activity in the extracts, such RNAs appeared to be efficiently 5'-truncated prior to translation. The observed levels of initiation on differently truncated templates suggested that a region in the middle of the poliovirus 5'-UTR is essential for the cap-independent initiation of viral polyprotein synthesis. The data reported here, in conjunction with the results from other laboratories, permitted to relate the essential cis-acting control elements to the 5'-UTR secondary structure domains defined previously (E.V. Pilipenko et al., Virology 168, 201-209). However, the removal of these domains activated another mode of polyprotein initiation, which appeared to require another set of translation initiation factors.

Base Sequence↗

PubMed1995

Retroviral vector-transduced cells expressing the core polyprotein induce feline immunodeficiency virus-specific cytotoxic T-lymphocytes from infected cats.

The core polyprotein of feline immunodeficiency virus (FIV) was expressed in primary feline T-lymphocytes using a retroviral vector. These cells were used as antigen-presenting stimulator cells (APSC) for the in vitro induction of cytotoxic T-lymphocytes (CTL) from feline peripheral blood mononuclear cells (PBMC). CTL from 4 cats chronically infected with the Petaluma strain of FIV specifically lysed autologous FIV-infected targets in an MHC-restricted manner. The CD8 phenotype of more than 70% of the induced effector cells (97% for cells from one cat) was consistent with MHC class I-restricted cytotoxicity. In addition, it was possible to detect low levels of core polyprotein-specific lysis from effector cells of two of the FIV-infected cats. When observed, the level of lysis, measured as a percentage of specific 111In release, was lower for the transgenic gag-expressing targets than for FIV-infected targets. The difference in killing may reflect the low level of core CTL were not detected in either PBMC stimulated with cells transduced by a retroviral vector without the FIV gag sequence or PBMC from an uninfected cat stimulated with autologous transgenic APSC. The detection of FIV-specific CTL from infected cats following stimulation with transgenic APSC suggests a role for retroviral vectors in determining CTL specific for individual lentiviral proteins in protective immunity.

3T3 Cells↗

PubMed1994

Processing of hepatitis C viral polyprotein in Escherichia coli.

Two proteinase activities, encoded by hepatitis C virus (HCV), Cpro-1 and Cpro-2. Cpro-1 and Cpro-2 appear to process the precursor polyprotein from which they originate. Mutant HCV polypeptides containing the region for these proteinases were produced in Escherichia coli as fusion proteins. The N- and C-terminal ends of the HCV polypeptides were fused with the E. coli maltose-binding protein (MBP) and E. coli dihydrofolate reductase (DHFR), respectively. The proteinase activities cleaved the fusion polypeptides by the same processing pathway used in eukaryotic protein production systems. The N-terminal amino acid (aa) sequences of the processed fusion proteins were determined. A comparison of those N-terminal sequences with the aa sequence of the HCV precursor polyprotein showed that the N-terminal and C-terminal cleavage sites of p70(NS3), one of the HCV nonstructural (NS) proteins, were the same as those identified in other processing studies: cleavages were estimated to be between aa 1026 and 1027 and between aa 1657 and 1658 of the HCV precursor protein, which are known to be cleaved by Cpro-1 and Cpro-2, respectively. Cpro-1 and Cpro-2 both functioned in E. coli and possessed authentic characteristic features.

ATP-Binding Cassette Transporters↗