Purification of a Soluble Template-Dependent Rhinovirus RNA Polymerase and Its Dependence on a Host Cell Protein for Viral

JOURNAL OF VIROLOGY, Jan. 1985, p. 266-272 22-538X/85/1266-7$2./ Copyright 1985, American Society for Microbiology Vol. 53, No. 1 Purification of a Soluble Template-Dependent Rhinovirus RNA Polymerase and Its Dependence on a Host Cell Protein for Viral RNA Synthesis CASEY D. MORROW, JOHN LUBINSKI, JANET HOCKO, GWENDOLYN F. GIBBONS, AND ASIM DASGUPTA* Department of Microbiology and Immunology and Jonsson Comprehensive Cancer Center, UCLA School of Medicine, Los Angeles, California 924 Received 13 July 1984/Accepted 1 October 1984 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 templateprimer. 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,-dalton protein purifies with both poly(u) polymerase and replicase activities. The single-stranded RNA genome of rhinovirus is replicated by a virus-specific RNA-dependent RNA polymerase found in cells infected with rhinoviruses (9, 26). The replication of rhinovirus RNA in infected cells is believed to be similar to that of other picornaviruses (2, 7). The input virus RNA is translated to produce an RNA-dependent RNA polymerase, which then replicates the genomic RNA in a two-step process. First, the genomic RNA (plus strand) acts as a template for the synthesis of complementary virus RNAs (minus strands), and then these minus strands serve as templates for the synthesis of progeny plus strands. Three RNA species have been recognized in cells infected with rhinovirus types 2 and 14 (2, 23, 24, 3). These species consist of single-stranded RNA, the replicative form, and the replicative intermediate. The single-stranded RNA is of similar length and structure to genomic RNA (2, 23, 3), and the replicative intermediate and replicative form are, respectively, multistranded and double-stranded structures (23). It is generally thought that the replicative intermediate consists of a full-length single-stranded RNA with several daughter strands which are in the process of synthesis. RNA polymerase(s), isolated from membrane-bound complexes in rhinovirus-infected cells, directs the in vitro synthesis of both single- and double-stranded RNAs (21, 34). This activity, however, measures largely the elongation of RNA synthesis rather than the initiation, since the complex represents RNA polymerase bound to viral RNA template in which RNA chains have already been initiated. In an attempt to gain more insights into rhinovirus RNA replication, we purified a virus-specific RNA-dependent RNA polymerase from HeLa cells infected with human rhinovirus type 2 (HRV-2). This enzyme is able to initiate copying of rhinovirus RNA in vitro. The RNA synthesized de novo is complementary to viral RNA template. Although a partially purified preparation of rhinovirus RNA polymerase copies virion RNA without an added primer, a more purified preparation is completely inactive in copying virion * Corresponding author. 266 RNA unless it is provided with a HeLa cell protein (host factor) or a synthetic oligouridylic acid [oligo(u)] primer. In this communication, we also show that a viral protein with an apparent molecular weight of 64, purifies with rhinovirus RNA-dependent RNA polymerase activity. MATERIALS AND METHODS Cells and viruses. HeLa cells were grown in suspension culture (minimal essential medium containing 1% newborn calf serum). HRV-2 strain HGP was obtained from the American Type Culture Collection, Rockyille, Md. Initially, HRV-2 was propagated in HeLa cell monolayer cultures six to seven times. Partially purified viruses obtained from monolayer cultures were then adapted to grow in suspension cultures with Joklik minimal essential medium containing 1% newborn calf serum. After the fifth passage through suspension culture of HeLa cells, a virus titer of ca. 11 PFU/ml was obtained. This preparation was used as the virus stock. Virus infection. Suspension cultures pf HeLa cells were infected with HRV-2 at a multiplicity of infection of 8 to 1 PFU per cell. Virus was adsorbed for 3 min at room temperature. Minimal essential medium containing 1% newborn calf serum was then added to the cell suspension, and infection was carried out at 34.5 C. Actinomycin D was added to a concentration of 5,ug/ml in experiments in which it was desirable to inhibit host RNA synthesis. For enzyme preparation, infections were stopped at 7 h and 1, ml of cells (4 x 15 cells per ml) was collected by centrifugation, washed once in Earle saline, and suspended in 1 ml of 1 mm Tris-hydrochloride (ph 7.5)-1 mm NaCl-1.5 mm MgCl2. A cytoplasmic extract was prepared by breaking the cells in a Dounce homogenizer. The extract was centrifuged at 2, x g for 3 min; the supernatant was considered fraction l. Purification of replicase: phosphocellulose chromatography. Phosphocellulose was prepared by the method of Burgess (8). A column (1 by 2 cm) was equilibrated with buffer A (5 Downloaded from http://jvi.asm.org/ on November 25, 218 by guest

VOL. 53, 1985 mm Tris-hydrochloride [ph 8.], 2% [vol/voll glycerol,.5% Nonidet P-4, 5 mm 2-mercaptoethanol). Fraction I was diluted 1:1 with buffer A and loaded on the column at a flow rate of 18 mi/h. The column was then thoroughly washed with buffer A, and protein was eluted with a linear gradient of to 1 M KCl in buffer A. Fractions were assayed for polyadenylic acid [poly(a)] oligo(u)-directed polyuridylic acid [poly(u)] polymerase activity as well as rhinovirion RNA-dependent RNA replicase activity. The active fractions were pooled, concentrated against solid sucrose to one-third their original volume, and dialyzed overnight against buffer A (fraction II). Replicase prepared this way was stable when stored at -7 C for 2 months, with 1 to 2% loss of activity. Poly(U)-Sepharose chromatography. A poly(u)-sepharose 4B column (.8 by 1 cm) was washed thoroughly with 2 M KCl before use. The column was then equilibrated with buffer B (buffer A containing 5 mm KCI). Fraction II enzyme was diluted 1:1 with buffer B and applied to the column at a flow rate of 6 ml/h. The column was thoroughly washed with buffer B. Proteins bound to the column were eluted either batchwise with buffer A containing.25 M KCl or with a linear gradient of 5 to 4 mm KCl in buffer A. Fractions were assayed for poly(u) polymerase activity and rhinovirion RNA-dependent replicase activity. Active fractions were pooled, concentrated, and dialyzed against buffer A to yield fraction III (for batch-eluted) or fraction IV (for gradient-eluted) enzyme. Polymerase prepared this way lost 1 to 2% activity when stored at -7 C for 6 weeks. Purification of host factor. Purification of host factor from uninfected HeLa cells to apparent homogeneity was as previously described (11). Purified host factor showed a single 67,-dalton band on sodium dodecyl sulfate (SDS)- gel electrophoresis followed by Coomassie blue staining. Rhinovirion RNA. Infected cells were collected at 1 to 11 h postinfection, washed once in Earle saline, and suspended in cold 1% Nonidet P-4-1 mm Tris-hydrochloride (ph 8.)-1 mm NaCl. The nuclei were removed by centrifugation at 5, x g for 5 min, and the virions were collected by centrifugation at 45, rpm for 2 h in a Beckman type 65 rotor. Virions were suspended in 1 mm Tris-hydrochloride (ph 7.5)-.1 M NaCl-.1 M EDTA-.1% SDS and were purified by sucrose density gradient centrifugation (31). Gradients were fractionated, and optical density at 28 nm was determined for each fraction. Virus peaks sedimenting at ca. 15S were pooled and sedimented again with a Beckman type 65 rotor. The virus pellet was suspended in 1 mm Tris-hydrochloride (ph 7.5)-l mm EDTA. Viral RNA was prepared by phenol extraction (three times). The RNA was precipitated in 7% ethanol and stored at -7 C in small portions. The integrity of rhinovirus RNA was checked by agarose gel electrophoresis under denaturing conditions (1). The RNA migrated as a single band at ca. 34S. All buffer solutions used in RNA purification procedure were treated with.1% diethylpyrocarbonate and autoclaved. Enzyme assays. The poly(a) oligo(u)-dependent poly(u) polymerase activity was assayed for 3 min at 3 C as described by Flanegan and Baltimore (17). For rhinovirion RNA-dependent replicase activity, the standard incubation mixture contained, in a total volume of 5,ul, 5 mm HEPES (N-2-hydroxyethylpiperazine-N'-2-ethanesulfonic acid)- KOH (ph 7.6), 3 mm magnesium acetate, 5,uM ZnC12, 4 mm dithiothreitol, 1 jig of actinomycin D per ml,.2 mm each of three other ribonucleoside triphosphates, 1 to 6,uM [a-32p]utp (specific activity, 2, to 5, cpm/pmol), and.5 to 1.,ug of fraction III replicase as defined above. IN VITRO REPLICATION OF HUMAN RHINOVIRUS 267 2. CWo) Q) 5 r - 3..-.~ ~ 4 1 8 1 2~~~~~+ Mg [mm ] FIG. 1. Effect of Mg2+ concentration on rhinovirus replicase activity. Ten micrograms of fraction 11 replicase was assayed at various concentrations of magnesium acetate in the presence of () or absence () of added rhinovirion RNA. Host factor-dependent replicase activity was assayed essentially the same way as the partially purified replicase activity, except that 1 to 2 p.g of fraction IV replicase and.1,ug of fraction VII host factor (11) were used. RNA synthesis in the presence of only fraction IV replicase served as the control. Incubation was for 1 h at 3 C. The labeled products were collected on membrane filters (.45,um) after precipitation with 7%t trichloroacetic acid in the presence of 1,ug of added carrier RNA. The filters were dissolved in 5 ml of Bray scintillation fluid (New England Nuclear Corp.) and counted. Materials. All chemicals, unless otherwise stated, were purchased from Sigma Chemical Co., St. Louis, Mo. Unlabeled nucleotides were obtained from Calbiochem-Behring, La Jolla, Calif. Poly(A) was purchased from Miles Laboratories, Inc., Elkhart, Ind. Oligo(U)1 2 was purchased from Collaborative Research, Inc., Waltham, Mass. Poly(U)- Sepharose 4B was obtained from Pharmacia Fine Chemicals, Inc., Piscataway, N.J. Phosphocellulose was purchased from Whatman, Inc., Clifton, N.J. All radioisotopes were purchased from New England Nuclear Corp., Boston, Mass. RESULTS Isolation of soluble, template-dependent rhinovirus replicase. To examine whether a virus-specific RNA-dependent RNA polymerase (replicase) activity could be purified from the soluble phase of cells infected with HRV-2 which can copy exogenously added rhinovirion RNA, we purified it by phosphocellulose chromatography. The soluble form of the enzyme was chosen because it is more readily purified and quite stable. Moreover, previous studies with poliovirus RNA polymerase have shown that it can be readily purified from the cytoplasm of infected cells (13, 19). Figure 1 shows the ability of the phosphocellulose-purified enzyme to copy rhinovirion RNA (plus strand) as a function of Mg2+ concentration. In the presence of Mg2+, the enzyme was able to Downloaded from http://jvi.asm.org/ on November 25, 218 by guest

268 MORROW ET AL. J. VIROL. TABLE 1. Hybridization of replicase product to different RNAs" Added RNA ~~~~~~~% Ribonuclease Added RNA resistance None... 23 Rhinovirus type 2... 1 Rhinovirus type 1... 26 Globin messenger...... 24 Brome mosaic virus... 23 Total HeLa mrna...... 2 a [32PICMP-labeled product of fraction II (phosphocellulose purified) rhinovirus replicase copying rhinovirus type 2 RNA was prepared. The doublestranded RNA product was isolated by phenol extraction after treatment of in vitro-synthesized RNA with pancreatic RNase as described previously (13). About 3 ng (2, cpm) of double-stranded RNA product was dissolved in 2,ul of water and boiled for 5 min in the presence of 5 ng of the indicated added RNA. The mixture was adjusted to.5% SDS-.45 M NaCl-.45 M sodium citrate and allowed to hybridize at 7 C for 1 h. The sample was chilled and divided into equal portions. One portion was treated with 1,ug of pancreatic RNase per ml and 2 U of Ti RNase per ml. Acid-precipitable radioactivity was determined. Background radioactivity from a boiled but unannealed sample was subtracted (ca. 5%), and the percent RNase resistance was calculated. incorporate UMP in response to the addition of rhinovirus RNA. Maximum incorporation of UMP was observed at a Mg2+ concentration of 1 to 4 mm. No incorporation was apparent in the absence of added rhinovirus RNA, implying that RNA-dependent RNA synthesis was occurring. All four ribonucleoside triphosphates were needed for optimal activity (data not shown), indicating heteropolymeric RNA synthesis. The Mg2+ optimum for rhinovirus RNA-dependent RNA synthesis was quite broad (Fig. 1). o E o CL X L-_ (i) AS 6 c L 12 E l a'.'~~~~~~~~~~~~)c D ca -Y-V X-X-y cc a. 2 4 6 Hours after infection FIG. 2. Time course of appearance of rhinovirus replicase. From a culture of rhinovirus type 2-infected cells containing 5,ug of actinomycin D per ml, 4 x 18 cells were removed at the indicated times and a replicase preparation through fraction II was prepared for each time point. Assays for replicase activity (-) with rhinovirus RNA or poly(u) polymerase activity (A) with poly(a) * oligo(u) were incubated at 3 C for 1 h and 3 min, respectively. Replicase activity of proteins prepared from mock-infected cells (x) was performed at 3 C for 1 h. RNA synthesis in the infected culture was measured by adding [3H]uridine (.5,uCi/ml) to a portion of the culture and determining the amount of radioactivity incorporated into acid-insoluble material in.1-ml aliquots of the culture taken at the indicated times (). To determine whether the product of RNA synthesis was a copy of the added viral RNA, we isolated, denatured, and renatured the RNase-resistant product from an in vitro reaction, either by itself or in the presence of either HRV-2 RNA or heterologous RNAs (Table 1). HRV-2 RNA could drive all of the product into a RNase-resistant form, whereas the self-annealed product or the product annealed with heterologous viral or cellular RNAs showed only ca. 25% RNase resistance. This background could be due to partial renaturation of the labeled product with the large molar excess of unlabeled rhinovirion template RNA present in the reaction. Replicase activity is rhinovirus specific. To determine whether the replicase activity was specific to infected cells, we prepared cytoplasmic extracts from infected and mockinfected cells at various times after infection or mock infection. Enzyme was then prepared by eluting infected or mock-infected extracts through phosphocellulose for each time point. No replicase activity was detected in the eluates of mock-infected extracts (Fig. 2). The rhinovirus-specific RNA-dependent replicase activity was first detected at ca. 4 h after infection and increased almost linearly until 7 h after infection. The first increase in enzynce activity coincided with the virus-specific RNA synthesis as measured by actinomycin D-resistant incorporation of [3H]uridine in infected cells (Fig. 2). Similar results were reported for the endogenous rhinovirus replicase activity catalyzed by replicase-template complex (34). A poly(a) oligo(u)-dependent poly(u) polymerase activity also coincided with the replicase and virus-specific RNA synthesis activities (Fig. 2). This activity was not present in uninfected cells and was not induced by mock infection of cells (data not shown). The poly(a) oligo(u)-dependent poly(u) polymerase activity was first detected in poliovirus-infected cells (17), and this activity is ~~~~~~~~~~~~~~ now believed to be associated with poliovirus replicase protein P63 (NCVP-4) (6, 32). co O Further purification and characterization of replicase. The - phosphocellulose-purified (fraction II, Table 2) rhinovirus ~~~~~~~~~~~~ replicase could be further purified by binding to poly(u)- agarose in low salt and eluting with.25 M KCl (fraction III, ~~~~~~~~~1 Table 2). This yielded a fraction ca. 3-fold purified over the 4)~~~~~~~~~~~~. crude extracts (Table 2). Both rhinovirion RNA-dependent replicase and poly(a) oligo(u)-dependent poly(u) polymerase activities co-eluted from the column (data not shown). E ~~~~~~~~~~~~~~~~18 Attempts to elute the enzyme with a linear salt gradient, however, resulted in complete loss of replicase activity, whereas poly(u) polymerase activity was still evident (Fig. TABLE 2. Purification of rhinovirus-specific poly(u) polymerase" Total Total S t Purifi- y Fraction protein activity (U/mg) cation (mg) (U)b (fold) I. S2 5 3, 6 1 1 II. Phosphocellulose 4 2, 5, 8 75 III. Poly(U)-Sepharose 5 1, 2, 33 33 batch elution IV. Poly(U)-Sepharose 1 59, 59, 98 2 gradient elution arhinovirus type 2-infected HeLa cells were collected 7 h after infection, and viral poly(u) polymerase was purified by the method described in the text. b One unit of poly(u) polymerase activity is defined as the amount of protein required to catalyze the incorporation of 1 pmol of labeled UMP into acid-precipitable form at 3 C for 3 min under the poly(u) polymerase assay conditions (17). Downloaded from http://jvi.asm.org/ on November 25, 218 by guest

VOL. 53, 1985 3). Purification of poly(u) polymerase by means of gradient elution from poly(u)-agarose gave an overall 1-fold enrichment of poly(u) polymerase activity (Table 2). We have designated the final fraction as fraction IV poly(u) polymerase. When individual fractions containing [35S]methioninelabeled viral proteins from the poly(u)-agarose column (gradient elution) were analyzed by SDS-polyacrylamide gel electrophoresis, only one viral protein having an approximate molecular weight of 64, was found to correspond exactly to poly(u) polymerase activity (Fig. 3). The best studied picornaviral replicase is that of poliovirus (4, 11, 13, 15, 17-19, 32, 33). In its purified form, the poliovirus RNA polymerase requires a host cell protein (host factor) to copy viral RNA in vitro (15). To determine z C- CL cc uz l- CL C- B..4 6 8 1 12 14 16 FRACTION NUMBER t-94 4-\6-6 7 s-43 FIG. 3. Analysis of viral proteins present in fractions [from a poly(u)-sepharose 4B column] having rhinovirus-specific poly(u) polymerase activity. (A) Rhinovirus proteins were labeled with [35S]methionine (1,7 Ci/mmol, 2 mci per 4 x 18 cells; New England Nuclear Corp.) by the procedure described by Yin and Lomax (35). Purification of poly(u) polymerase through phosphocellulose, poly(u)-sepharose 4B (step elution), and poly(u)- Sepharose 4B (gradient elution) was carried out as described in the text. Fractions from the final poly(u)-sepharose 4B (fraction IV, Table 2) column were assayed for poly(u) polymerase activity () as described by Flanegan and Baltimore (17) and for rhinovirion RNA-dependent replicase activity (). Labeled products were collected on membrane filters and counted. (B) Corresponding fractions containing [35S]methionine-labeled viral proteins were analyzed on a 12.5% SDS-polyacrylamide gel (28) alongside [35S]methionine-labeled rhinovirus-infected extract (extreme right lane). The gel was fixed with 1% acetic acid and fluorographed, and then an autoradiogram was prepared. Migrations of standard protein markers on the same gel are indicated. IN VITRO REPLICATION OF HUMAN RHINOVIRUS 269 whether rhinovirus replicase activity is also dependent on host factor, we pooled and concentrated fractions (numbers 8 to 12, Fig. 3) containing poly(u) polymerase activity and tested the concentrated enzyme for its ability to copy viral RNA in the absence and presence of host factor. The concentrated enzyme was still inactive in copying virion RNA (Fig. 4A). However, when purified host factor was added to this fraction, it completely reconstituted replicase activity (Fig. 4A). RNA synthesis in response to rhinovirion RNA increased linearly with increasing concentrations of poly(u) polymerase in the presence of a saturating amount of host factor. When the viral polymerase was omitted from the reaction, there was virtually no RNA synthesis, indicating that both viral and host components were necessary for RNA synthesis. Oligo(U), a synthetic primer, was able to substitute for host factor (Fig. 4C). RNA synthesis in the presence of a constant amount of viral polymerase increased linearly with increasing concentrations of host factor or oligo(u) (Fig. 4B and C). Oligo(U) was maximally active at a ratio of 5 mol of oligo(u) to 1 mol of rhinovirion RNA and was inhibitory at higher concentrations. Poliovirus-specific RNA-dependent RNA polymerase also utilizes oligo(u) for copying of poliovirion RNA. However, with poliovirus replicase, maximal stimulation is observed at an oligo(u) to poliovirion RNA ratio of 2:1 (15). Stimulation of replicase activity by host factor is dependent upon the initial concentration of host factor. At low concentrations of host factor, the rate of synthesis is proportional to the host factor concentration. A typical time course for the host factor-dependent replicase reaction is shown in Fig. 5A. The reaction was linear for almost 3 h, after which RNA synthesis reached a plateau. The ph optimum for rhinovirus replicase reaction was quite broad (Fig. SB). Maximal RNA synthesis was observed at ph 7.6. Eighty to 9% of total RNA was synthesized at ph values as low as 7.4 and as high as 8. compared with the value at ph 7.6. The ph optimum for poliovirus replicase was previously found to be quite sharp at ph 8. (unpublished data). Like poliovirus replicase, rhinovirus RNA replicase was quite sensitive to salt. Over 9% RNA synthesis was inhibited at 5 mm KCl (Fig. 6A). For poliovirus replicase, however, 1 mm KCl was required to obtain an 8 to 9% inhibition of RNA synthesis (13). Similar results were obtained for both rhinovirus and poliovirus replicases with NaCl (data not shown). In contrast to monovalent salts, Zn2+ (in the form of ZnC12) was found to stimulate host factor-dependent rhinovirus replicase activity (Fig. 6B). This stimulation was concentration dependent. A maximal stimulation of fourfold, compared with the control without Zn2+, was observed at 5,uM Zn2+. However, Zn2+ was not able to substitute for Mg2+ (data not shown). The effect of Zn2+ was most probably at the level of RNA chain elongation, since oligo(u)- primed copying of both pure poly(a) and rhinovirion RNA was stimulated by zinc (data not shown). Template specificity of rhinovirus replicase. To examine the template specificity of the replicase, we tested the most purified (fraction IV, Table 2) enzyme preparation for its ability to copy a number of RNAs. In the presence of purified host factor, the fraction IV replicase did not show much specificity in copying rhinovirion RNA over other poly(a)-containing RNA templates (Table 3). Although rhinovirion RNA was copied with the highest efficiency, the replicase also copied poliovirion RNA and globin mrna with an efficiency of 5 to 6% compared with that with Downloaded from http://jvi.asm.org/ on November 25, 218 by guest

27 MORROW ET AL. J. VIROL. E Cl) A ~~~~~~~~~~~~~~~~9 4) o 3 t 3 6. a. ~~~~~~~~~~~~~~3- a-i.5 1. 1.5.12.24.36 OA8 1 2 3 4 Aug Poly(U)polymerase Aug Host factor pmole Oligo(U) FIG. 4. Requirement for rhinovirus RNA-dependent replicase activity. (A) Reactions in a 5->±l volume were carried out by using 1,ug of rhinovirion RNA for 1 h at various concentrations of fraction IV poly(u) polymerase in the absence () or presence () of.36 p.g of fraction VII host factor (11). (B and C) Similar reactions were carried out with various concentrations of either fraction VII host factor (B) or oligo(u) (C) in the absence () or presence () of 1 p.g of fraction IV poly(u) polymerase. rhinovirus RNA. With brome mosaic virus RNA as a template lacking the 3'-terminal poly(a) tail, however, the copying was significantly less (Table 3). DISCUSSION It is evident that the soluble fraction of rhinovirus-infected cells contains a virus-specific RNA replicase activity that can be purified to demonstrate copying of exogenously added rhinovirion RNA in vitro. Detection and purification of this RNA replicase was greatly facilitated by an assay for poly(u) polymerase activity in response to poly(a) oligo(u). Even the purest replicase preparation. ' Cu. C.) E 6 37A 7.2 C a- 2- B contains this activity (Fig. 3), implying that the replicase and poly(u) polymerase are probably closely related activities. The soluble replicase activity contains mainly one viral protein with an approximate molecular weight of 64, (P64) (Fig. 3). However, in some preparations we detected two other viral proteins of approximate molecular weights 74, and 45,. These two proteins can also be detected in the [35S]methionine-labeled viral replicase preparation shown in Fig. 3, but only after pooling and concentrating peak fractions and overexposing the autoradiogram. The rhinovirus-specific P64 may be analogous to poliovirus RNA polymerase (P63) that has already been shown to contain both replicase and poly(u) polymerase activities (6, 32). It is clear that when the rhinovirus replicase preparation described here is further purified, the enzyme becomes dependent on an added protein factor found in uninfected E C,. 16 A B C)12- o 8-. Downloaded from http://jvi.asm.org/ on November 25, 218 by guest a-i 1 2 3 7.2 7.6 8. 8.4 Hours ph FIG. 5. Kinetics and ph optimum of rhinovirion RNA-dependent RNA synthesis catalyzed by viral poly(u) polymerase and host factor. (A) One microgram of fraction IV poly(u) polymerase was incubated with.3,ug of fraction VII host factor (11) under RNA synthesis assay conditions. The reactions were stopped at the indicated times and processed. (B) Rhinovirion RNA-dependent RNA synthesis was carried out as described in A, except that the ph of the buffer solution was varied as indicated. Both Tris-hydrochloride and HEPES-KOH buffers gave similar results. '.4 4-2 4 6 8 o1 2 4 6 8 1 mm KCI pjm Zn +2 FIG. 6. Effect of KCI and Zn2+ on rhinovirus replicase activity. (A) Rhinovirion RNA-dependent RNA synthesis was carried out as described in the legend to Fig. 5, except that the indicated amounts of KCI were added at the start of reactions. (B) Rhinovirion RNA replicase activity was determined in the absence or presence of the indicated amounts of ZnC12.

VOL. 53, 1985 TABLE 3. Template specificity of rhinovirus replicasea Fraction IV [32PJUMP poly(u) Host factor RNA incorporation polymerase (pmol) + + None.4 + + Rhinovirus 2.1 + + Poliovirus 1.3 + + Globin 1.2 + + BMVb.66 + - Polio/Rhino/Globin/BMV.7 - + Polio/Rhino/Globin/BMV.4 a Reaction mixtures contained 1 p.g offraction IV rhinovirus RNA polymerase, 1,ug of various RNAs as indicated, and.1,ug of purified host factor. Assay conditions were the same as described in the text. b BMV, Brome mosaic virus. cells (host factor [14, 15]). This is not surprising because we previously showed that the same host cell protein was required for replication of poliovirion RNA in vitro (4, 12, 15). Host factor is a single polypeptide of apparent molecular weight 67, (3, 11). Most of this protein is soluble; however, 3% of total host factor is found associated with ribosomes (12). The host factor estimated to be present at 5, to 1, copies per cell (3, 12) interacts physically with poliovirus replicase (3, 12). Our unpublished results indicate that this protein is present in phosphocellulosepurified rhinovirus replicase preparation. During salt gradient elution from poly(u)-sepharose 4B, the host factor activity elutes before virus-specific polymerase activity (data not shown). The rhinovirus replicase activity can be reconstituted by combining this host factor activity with viral polymerase from the same column. This result strongly suggests that replicase itself has not simply been altered during purification and that host factor activity was indeed present in the starting material. Consistent with this notion is the result that nonspecific proteins like bovine serum albumin or ovalbumin do not stimulate rhinovirus replicase activity (data not shown). At its present stage of purity, the rhinovirus replicase does not show any significant preference for rhinovirus RNA as a template. It copies other RNAs, both viral and cellular. This is puzzling, because the viral replicase apparently specifically copies viral RNA in the cytoplasm of infected cells. The reason for this is not clear, but it could be due to contaminating host proteins in the preparation. Alternatively, the replicase used in these experiments may be deficient in a protein required for specific copying of the rhinovirus RNA template. The rhinovirus replicase copies a synthetic homopolymer, poly(a), in the presence of a synthetic primer, oligo(u). At present, we do not know whether other homopolymeric RNAs like poly(g), poly(c), and poly(u) will be copied by the replicase in the presence of appropriate primers. How the replicase initiates copying of viral RNA template remains obscure. For poliovirus RNA replication, results from our laboratory as well as others suggest that a precursor(s) to poliovirus genome-linked protein may act as a primer for initiation of poliovirus minus-strand RNA synthesis (5, 28, 29). It is not known at present whether there is a similar protein attached to the 5' terminus of rhinovirus RNA. Clearly, more studies are required to answer this question. Our preliminary experiments in characterizing the products of in vitro replicase reaction have revealed the production of labeled crna molecules as big as 28S. So far, we IN VITRO REPLICATION OF HUMAN RHINOVIRUS 271 have not been able to synthesize complete, full-length copies of the template RNA. At present we do not know the reason for this. One possibility is the limited degradation of the input viral RNA in the in vitro reaction. However, the replicase and host factor preparations used in these studies do not contain detectable amounts of RNase (data not shown). To date, the best studied picornaviral replicase is that of poliovirus. There are some very interesting similarities between poliovirus and rhinovirus replicases. First, in their purified forms, both polymerases are dependent on the same host cell protein (host factor). For both of these enzymes, the requirement for host factor can be met by a synthetic primer, oligo(u). With poliovirus RNA polymerase, oligo(u) was shown to prime RNA synthesis by binding to the poly(a) tract at the 3' end of viral RNA (4, 33). We assume, although we have not shown, that rhinovirus replicase can elongate an oligo(u) primer hydrogen bonded to the 3'- terminal poly(a) tract of rhinovirion RNA. Both polio- and rhinovirus polymerases are stimulated by Zn2+ and inhibited by monovalent salts. It is interesting to note that all nucleic acid polymerases examined to date have been zinc-containing enzymes (27). It is possible that zinc is partially or totally removed during purification of rhinovirus replicase and so the purified enzyme shows a requirement of zinc for its activity. In this context, it is important to note that chelating agents that specifically chelate zinc inhibits residual poliovirus replicase activity in the absence of zinc (4). It is surprising to find most of the replicase in the soluble phase of the cell, because viral RNA replication occurs on cellular membranes (1). A reasonable explanation, as noted previously by Dasgupta et al. (13), is that initiation of RNA synthesis occurs by interaction of soluble replicase and viral RNA and thereafter the complex may bind to membranes. This explanation is consistent with the facts that all templatedependent picornavirus replicase preparations reported to date have been cytoplasmic (3, 11, 13, 15, 17-19, 32; this report) and the majority of the host factor is localized in the soluble phase of cells (3, 12). Moreover, it is worth mentioning that the in vitro system reported here synthesizes minus strands, whereas previous studies on intracellular viral RNA synthesis have concentrated mainly on plus-strand synthesis. The requirements for plus-strand synthesis and minusstrand synthesis could be significantly different, as noted previously for the replicases of RNA bacteriophages (16, 22, 25) Ḟinally, the establishment of a template-dependent replication system from HRV-2-infected cells gives us an opportunity to compare the mechanism of initiation of RNA replication by two viruses, rhinovirus and poliovirus, both belonging to the picornaviridae family. ACKNOWLEDGMENTS C.D.M. was supported by a Public Health Service fellowship grant CA 956-9 from the National Cancer Institute. A.D. is a member of the Molecular Biology Institute at UCLA. This work was supported by a Public Health Service grant from the National Institute of Allergy and Infectious Diseases (Al 18272) to A.D. 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