Identification of poliovirus polypeptide P63 as a soluble RNA-dependent RNA polymerase

Poliovirus RNA-dependent RNA polymerase and host cell protein synthesize product RNA twice the size of poliovirion RNA in vitro

The poliovirus RNA-dependent RNA polymerase required an oligouridylate primer or a HeLa cell protein (host factor) to initiate RNA synthesis on poliovirion RNA in vitro. The polymerase synthesized template-sized product RNA in the oligouridylate-primed reaction. In the host factor-dependent reaction, the largest product RNA synthesized by the polymerase was twice the size of the template RNA. About half of the product RNA recovered from this reaction was shown to exist in the form of a snapback sequence. Time-course reactions and pulse-chase experiments showed that the product RNA was only slightly larger than the template RNA at early reaction times and that with time it increased in size to form the dimer-sized product RNA. Inhibition of the elongation reaction by adding only [alpha-32P]UTP and ATP resulted in the formation of template-sized product RNA. The dimer-sized product RNA was unaffected by phenol extraction or proteinase K treatment but was converted to template-sized molecules by S1 nuclease. Dimer-sized poliovirus RNA that was sensitive to S1 nuclease was also isolated from poliovirus-infected cells. The results from this study indicate that the labeled negative-strand product RNA synthesized in vitro was covalently linked to the positive-strand template RNA. Thus, in vitro, the primer-dependent poliovirus RNA polymerase may initiate RNA synthesis in the presence of the host factor by using the 3' end of the template RNA as a primer.

The host protein required for in vitro replication of poliovirus is a protein kinase that phosphorylates eukaryotic initiation factor-2

The HeLa cell protein (host factor) required for in vitro replication of poliovirus has been identified as a 67,000 dalton phosphoprotein. The purified protein displays three activities in vitro: stimulation of poliovirus RNA synthesis in the presence of poliovirus replicase, apparent self-phosphorylation, and phosphorylation of the alpha-subunit of eukaryotic protein synthesis initiation factor 2 (eIF-2). All three activities can be removed or inhibited by an antibody to host factor. Partially purified preparations of reticulocyte eIF-2 contain a similar phosphoprotein and display host factor activity in the viral RNA synthesis assay in vitro. In vitro phosphorylation of the 67 kd protein can be stimulated by low concentrations of double-stranded RNA. Addition of phosphorylated host factor in an in vitro RNA synthesis assay significantly changes the kinetics of viral RNA synthesis, indicating that protein phosphorylation may play an important role in viral RNA replication.

Purification of a soluble template-dependent rhinovirus RNA polymerase and its dependence on a host cell protein for viral RNA synthesis

The soluble phase of the cytoplasm of human rhinovirus type 2-infected cells contains an enzymatic activity able to copy rhinovirion RNA without an added primer. This RNA-dependent RNA polymerase (replicase) makes a specific copy of the added rhinovirion RNA, as shown by hybridization of the product to its template RNA but not to other RNAs. The same replicase preparation also contains a virus-specific polyuridylic acid [poly(U)] polymerase activity which is dependent on added polyadenylic acid-oligouridylic acid template-primer. Both activities purify together until a step at which poly(U) polymerase but no replicase activity is recovered. Addition of a purified HeLa cell protein (host factor) to this poly(U) polymerase completely reconstitutes rhinovirus replicase activity. Host factor activity can be supplied by adding oligouridylic acid, suggesting that the host cell protein acts at the initiation step of rhinovirus RNA replication. A virus-specific 64,000-dalton protein purifies with both poly(U) polymerase and replicase activities.

Recombination and rescue between temperature-sensitive mutants of poliovirus type 1

Four different temperature-sensitive (ts) mutants derived from the Mahoney strain of poliovirus type 1, were crossed in an infectious center recombination test. Evidence for recombination was obtained in three crosses, with a different segregation of an unselected marker, resistance to guanidine, in each case. Evidence for genetic complementation between ts mutants was not found, except with one set of RNA- mutants, ts 221 and ts 035. The marked virus yield enhancement which was observed in cells mixedly infected by these two mutants resulted from a nonreciprocal rescue of ts 035 by ts 221. The effects of ts 221 input multiplicity and of guanidine inhibition of viral RNA replication on the rescue were analyzed. The results showed that yield enhancement of ts 035 in mixed infection could be correlated to the low level RNA replication of ts 221 at the nonpermissive temperature.

ATP is required for initiation of poliovirus RNA synthesis in vitro: demonstration of tyrosine-phosphate linkage between in vitro-synthesized RNA and genome-linked protein

Poliovirus replicase- and host factor-catalyzed copying of 3'-terminal polyadenylic acid [poly(A)] of poliovirion RNA was studied. Host factor-stimulated synthesis of polyuridylic acid [poly(U)] by the replicase required ATP in addition to UTP. ATP was not required for the oligouridylic acid-primed copying of 3'-terminal poly(A) of virion RNA. GTP, CTP, and AMP-PCP (5'-adenylyl beta-gamma methylenediphosphate, an ATP analog) could not replace ATP in host factor-stimulated synthesis of poly(U). Antibodies to poliovirus genome-linked protein (VPg) specifically precipitated in vitro-synthesized poly(U) from a host factor-stimulated reaction. The poly(U) synthesized in a host factor-stimulated reaction was shown to be attached to VPg precursor polypeptide(s) via a tyrosine-phosphate bond as found in poliovirion VPg-RNA.

Structure of poliovirus replicative intermediate RNA. Electron microscope analysis of RNA cross-linked in vivo with psoralen derivative

The structure of the poliovirus replicative intermediate RNA was examined by electron microscopy after cross-linking in vivo with 4'-aminomethyl-4,5',8-trimethylpsoralen. After purification from infected cells, undenatured RI appeared as a double-stranded backbone of genome length, with an average of three (and occasionally up to eight) nascent, single-stranded tails. After denaturation, however, only single strands of heterogeneous length were visualized, indicating that the RI in the cell contains little or no duplex structure, and thus nascent chains are only transiently hydrogen-bonded to their template over short regions. The double-stranded backbone of undenatured RI, observed previously by others and in these experiments, is due to collapse of complementary chains during the deproteinization and purification procedures. The effectiveness of the in vivo cross-linking procedure was demonstrated by the complete inhibition of viral RNA synthesis in treated cells and by direct binding of [3H]AMT to RI molecules in vivo. Mature polio virions are impermeable to AMT; however, growth of virus in cells incubated with AMT in the dark resulted in normal yields of virus particles containing RNA genomes, whose infectivity could be subsequently photo-inactivated. The frequency of AMT-induced cross-linking was determined by analyses of double-stranded poliovirus RNA (RF). Cross-linking in vitro followed by spreading for electron microscopy under denaturing conditions yielded bubbled duplex structures with a minimum of one interstrand cross-link per 80 base-pairs. RF cross-linked in vivo also showed extensive cross-linking, decreased about fivefold from the in vitro cross-linked value. Thus, the failure to detect cross-linked RI under these conditions indicates that extensive base-pairing does not exist in vivo.

Antibody to poliovirus genome-linked protein (VPg) precipitates in vitro synthesized RNA attached to VPg-precursor polypeptide(s)

Antibody to poliovirus genome-linked protein VPg, specifically precipitated RNA synthesized in vitro by the poliovirus replicase and host factor in response to poliovirion RNA. A significant amount of the immunoprecipitated RNA was RNAase T1 resistant, sedimented at approximately 2-4 S and was shown to be largely polyuridylic acid. RNAase A digestion or alkali hydrolysis of the immunoprecipitated RNA left [32P]UMP-labeled material which comigrated on SDS-polyacrylamide gels with known VPg-precursor polypeptides. The results presented in this paper suggested that VPg was involved in the host factor-dependent, poliovirus replicase-catalyzed in vitro RNA synthesis, most probably in the form of a larger precursor protein.

Membrane-dependent uridylylation of the genome-linked protein VPg of poliovirus

A small nucleotidyl-protein has been synthesized in vitro in a membrane fraction of poliovirus-infected HeLa cells. Analyses of the nucleotides and polypeptide have shown that the nucleotidyl-protein is VPg-pUpU: the genome-linked protein of poliovirion RNA covalently bound to the first two 5'-terminal nucleotides of poliovirus RNA. Synthesis of VPg-pUpU in vitro was sensitive to nonionic detergent. We suggest that VPg-pUpU is part of the initiation complex in poliovirus RNA replication in a membranous environment.

Antibody to a synthetic nonapeptide corresponding to the NH2 terminus of poliovirus genome-linked protein VPg reacts with native VPg and inhibits in vitro replication of poliovirus RNA

A synthetic nonapeptide corresponding to the N-terminal sequence of poliovirus genome-linked protein (VPg) was linked to bovine serum albumin and used to raise antibodies in rabbits. The antipeptide antibodies specifically precipitated the nonapeptide, native VPg, and VPg-linked poliovirion RNA. The antipeptide antibodies inhibited host factor-stimulated, poliovirus replicase-catalyzed in vitro synthesis of full-length (35S) RNA in response to virion RNA. Oligouridylic acid-stimulated RNA synthesis was not affected by the antipeptide antibodies. Preincubation of the antibodies with excess nonapeptide reversed the antipeptide antibody-mediated inhibition of host factor-stimulated RNA synthesis by the poliovirus replicase. A role for VPg in the in vitro replication of poliovirus RNA genome is discussed.

Antibody to host factor precipitates poliovirus RNA polymerase from poliovirus-infected HeLa cells

An antibody to a host cell protein (host factor) which inhibited the host factor-dependent transcription of poliovirion RNA was used to characterize the immunoprecipitated proteins from both uninfected and poliovirus-infected HeLa cells. The antibody specifically precipitated a major protein of approximately 67,000 Da and a 40,000-Da minor protein from uninfected HeLa cells. The immune serum also specifically precipitated poliovirus RNA polymerase (P63, NCVP4) from poliovirus-infected HeLa cells indicating an association of the viral RNA polymerase with the host factor in vivo. A physical interaction between purified host factor and P63 could also be demonstrated in vitro. The antibody was further used to determine the distribution of host factor among different subcellular fractions of HeLa cells. Most of the cellular host factor was present in the cytoplasmic fraction (70%). Approximately 30% of the total host factor was found to be associated with the ribosomes.

Purification of host factor required for in vitro transcription of poliovirus RNA

A host cell protein (host factor) which is required for the in vitro transcription of poliovirus RNA has been purified to near homogeneity from an uninfected HeLa cell ribosomal salt wash. A single protein with an approximate molecular weight of 67,000 is associated with this "host factor" activity. The purified host factor catalyzes the synthesis of genome-length copies of poliovirion RNA in the presence of poliovirus RNA polymerase. Oligo(U) can replace host factor in this reaction. The RNA product synthesized in the presence of host factor is shown to be complementary to virion RNA.

Membrane fractions active in poliovirus RNA replication contain VPg precursor polypeptides

The poliovirus specific polypeptide P3-9 is of special interest for studies of viral RNA replication because it contains a hydrophobic region and, separated by only seven amino acids from that region, the amino acid sequence of the genome-linked protein VPg. Membraneous complexes of poliovirus-infected HeLa cells that contain poliovirus RNA replicating proteins have been analyzed for the presence of P3-9 by immunoprecipitation. Incubation of a membrane fraction rich in P3-9 with proteinase leaves the C-terminal 69 amino acids of P3-9 intact, an observation suggesting that this portion is protected by its association with the cellular membrane. These studies have also revealed two hitherto undescribed viral polypeptides consisting of amino acid sequences of the P2 and P3 regions of the polyprotein. Sequence analysis of stepwise Edman degradation show that these proteins are 3b/9 (Mr 77,000) and X/9 (Mr 50,000). 3b/9 and X/9 are membrane bound and are turned over rapidly and may be direct precursors to proteins P2-X and P3-9 of the RNA replication complex. P2-X, a polypeptide void of hydrophobic amino acid sequences but also found associated with membranes, is rapidly degraded when the membraneous complex is treated with trypsin. It is speculated that P2-X is associated with membranes by its affinity to the N-terminus of P3-9.

Poliovirus RNA synthesis in vitro: structural elements and antibody inhibition

The poliovirus RNA polymerase complex has been analyzed by immunoautoradiography using antibody probes derived from purified replicase (P3) region viral polypeptides. Antibody preparations made against the polio RNA polymerase, P3-4b, detected a previously unreported cellular protein that copurifies with the RNA polymerase. An IgG fraction purified from rabbit antiserum to polypeptide P3-2, a precursor of the RNA polymerase, specifically inhibits poliovirus RNA synthesis in vitro. We have also immunoprecipitated a 60,000-dalton protein (P3-4a) with antiserum to protein P3-4b and have determined the precise genomic map position of this protein by automated Edman degradation. Protein P3-4a originates by cleavage of the RNA polymerase precursor at a glutamine-glycine amino acid pair not previously reported to be a viral cleavage site.

Poliovirus RNA-dependent RNA polymerase synthesizes full-length copies of poliovirion RNA, cellular mRNA, and several plant virus RNAs in vitro

The poliovirus RNA-dependent RNA polymerase was active on synthetic homopolymeric RNA templates as well as on every natural RNA tested. The polymerase copied polyadenylate. oligouridylate [oligo(U)], polycytidylate . oligoinosinate, and polyinosinate. oligocytidylate templates to about the same extent. The observed activity on polyuridylate. oligoadenylate was about fourfold less. Full-length copies of both poliovirion RNA and a wide variety of other polyadenylated RNAs were synthesized by the polymerase in the presence of oligo(U). Polymerase elongation rates on poliovirion RNA and a heterologous RNA (squash mosaic virus RNA) were about the same. Changes in the Mg(2+) concentration affected the elongation rates on both RNAs to the same extent. With two non-polyadenylated RNAs (tobacco mosaic virus RNA and brome mosaic virus RNA3), the results were different. The purified polymerase synthesized a subgenomic-sized product RNA on brome mosaic virus RNA3 in the presence of oligo(U). This product RNA appeared to initiate on oligo(U) hybridized to an internal oligoadenylate sequence in brome mosaic virus RNA3. No oligo(U)-primed product was synthesized on tobacco mosaic virus RNA. When partially purified polymerase was used in place of the completely purified enzyme, some oligo(U)-independent activity was observed on the brome mosaic virus and tobacco mosaic virus RNAs. The size of the product RNA from these reactions suggested that at least some of the product RNA was full-sized and covalently linked to the template RNA. Thus, the polymerase was found to copy many different types of RNA and to make full-length copies of the RNAs tested.

Characterization of a temperature-sensitive defect of enterovirus type 70

The mechanism of the failure of enterovirus type 70 to replicate at a nonpermissive temperature (39 degrees C) was investigated, and the following results were obtained. (i) Viral RNA synthesis was not observed at 39 degrees C in LLC-MK2 cells, in accordance with our previous findings with primary monkey kidney cells (Miyamura et al., Intervirology 9:206-213, 1978). (ii) Shutoff of host cell macromolecular synthesis by virus infection was as efficient at 39 degrees C as at a permissive temperature (33 degrees C). This inhibitory effect similarly occurred even in the presence of guanidine hydrochloride. (iii) Viral protein synthesis proceeded in vivo at the nonpermissive temperature, and the rate of the protein synthesis was higher than that at the permissive temperature under the conditions in which sufficient viral mRNA had been accumulated. This was also confirmed by analyzing the intracellular proteins synthesized at the nonpermissive temperature by sodium dodecyl sulfate-polyacrylamide gel electrophoresis, which identified them as virus-specific proteins. (iv) When infected cells were incubated at 39 degrees C and then transferred to 33 degrees C, viral RNA synthesis took place even in the presence of cycloheximide. (v) Furthermore, in experiments performed with an in vitro cell-free assay system, viral polymerase activity was found in the membrane-bound preparation extracted from infected cells which had been incubated at 39 degrees C in the presence or absence of guanidine hydrochloride. These results indicate that early translation of mRNA proceeds normally at the nonpermissive temperature and that the temperature-sensitive defect resides in the transcriptional stage.

Antibodies against a synthetic peptide of the poliovirus replicase protein: reaction with native, virus-encoded proteins and inhibition of virus-specific polymerase activities in vitro

A carboxy-terminal peptide of the poliovirus replicase protein (p63) was chemically synthesized, coupled to bovine serum albumin carrier, and injected into rabbits. The resulting antisera reacted with six virus-specific proteins from HeLa cells infected with poliovirus: NCVP 0b, NCVP 1b, NCVP 2, a protein of about 60,000 daltons, p63, and NCVP 6b. The identity of the 60,000-dalton protein is not known, but the other results were consistent with previous experimental approaches which demonstrated that p63 and the other four polypeptides have common coding sequences. An amino-terminal peptide of p63 failed to elicit an immune response in rabbits. Antibodies raised against the p63 carboxy-terminal peptide inhibited poliovirus replicase and polyuridylic acid polymerase activities in vitro, providing strong support for earlier suggestions that these activities are a property of a single virus-specific polypeptide.

Isolation and preliminary characterization of temperature-sensitive mutants of poliovirus type 1

We isolated six temperature-sensitive mutants of poliovirus type 1 (Mahoney) by hydroxylamine mutagenesis and replica plating at 31, 33 (permissive), and 39 degrees C (restrictive). One of these mutants, designated tsB9, was chosen for more detailed examination. tsB9 accumulated 25% of the wild-type amount of virus-specific RNA at the restrictive temperature. We found that tsB9 was not able to synthesize mature, 35S single-stranded RNA at the restrictive temperature. In spite of the absence of significant RNA synthesis, tsB9 retained the ability to inhibit host protein synthesis during infection at 39 degrees C at about the same rate as wild-type virus.

Evidence for intramolecular self-cleavage of picornaviral replicase precursors

It has previously been shown that when encephalomyocarditis viral RNA is translated in cell-free extracts of rabbit reticulocytes, it synthesizes a virus-coded protease, p22, which is derived by cleavage of a precursor protein, C. Protein C is shown here to be cleaved by two different mechanisms, which were distinguished by their sensitivity to dilution. One mechanism was sensitive to dilution; the other was not. The biphasic cleavage behavior was unchanged by diluting incubation mixtures with untranslated reticulocyte extract instead of buffer, suggesting that both types of cleavage were mediated by virus translation products. It is proposed that the dilution-sensitive cleavage of protein C is due to a virus-coded protease, probably p22 itself, and that the dilution-independent cleavage is due to intramolecular self-cleavage of protein C.

Characterization of a 70S polyuridylic acid polymerase isolated from foot-and-mouth disease virus-infected cells

A polyuridylic acid polymerase complex isolated from foot-and-mouth disease virus-infected cells sedimented at 70S in a sucrose gradient and appeared in the exclusion volume of an agarose column whose molecular weight cutoff was 5 x 10(6). Phenol extraction of the complex yielded a heterogeneous band of virus-specific RNA and an apparently host cell-derived 4.5 to 5S RNA, both of which are essentially single stranded. Neither RNA served as a template in the cell-free enzyme reaction. Polyacrylamide gel analysis revealed five polypeptides with molecular weights of 50,000, 56,000, 60,000, 70,000, and 74,000 and with molar ratios of 1:2:2:1:1, respectively. Autoradiography showed P56 to be the only major virus-induced polypeptide; the other proteins are apparently of host cell origin. Electron microscopic examination suggested a cartwheel shape for the polymerase complex which was seen to dissociate as polyadenylic acid was added. Antibody previously shown to inhibit enzyme activity aggregated the 70S units.

Poliovirus replication proteins: RNA sequence encoding P3-1b and the sites of proteolytic processing

A partial amino-terminal amino acid sequence of each of the major proteins encoded by the replicase region (P3) of the poliovirus genome has been determined. A comparison of this sequence information with the amino acid sequence predicted from the RNA sequence that has been determined for the 3' region of the poliovirus genome has allowed us to locate precisely the proteolytic cleavage sites at which the initial polyprotein is processed to create the poliovirus products P3-1b (NCVP1b), P3-2 (NCVP2), P3-4b (NCVP4b), and P3-7c (NCVP7c). For each of these products, as well as for the small genome-linked protein VPg, proteolytic cleavage occurs between a glutamine and a glycine residue to create the amino terminus of each protein. This result suggests that a single proteinase may be responsible for all of these cleavages. The sequence data also allow the precise positioning of the genome-linked protein VPg within the precursor P3-1b just proximal to the amino terminus of polypeptide P3-2.