Temperature sensitive influenza A virus genome replication results from low thermal stability of polymerase-cRNA complexes
© Dalton et al; licensee BioMed Central Ltd. 2006
Received: 16 June 2006
Accepted: 25 August 2006
Published: 25 August 2006
The RNA-dependent RNA polymerase of Influenza A virus is a determinant of viral pathogenicity and host range that is responsible for transcribing and replicating the negative sense segmented viral genome (vRNA). Transcription produces capped and polyadenylated mRNAs whereas genome replication involves the synthesis of an alternative plus-sense transcript (cRNA) with unmodified termini that is copied back to vRNA. Viral mRNA transcription predominates at early stages of viral infection, while later, negative sense genome replication is favoured. However, the "switch" that regulates the transition from transcription to replication is poorly understood.
We show that temperature strongly affects the balance between plus and minus-sense RNA synthesis with high temperature causing a large decrease in vRNA accumulation, a moderate decrease in cRNA levels but (depending on genome segment) either increased or unchanged levels of mRNA. We found no evidence implicating cellular heat shock protein activity in this effect despite the known association of hsp70 and hsp90 with viral polymerase components. Temperature-shift experiments indicated that polymerase synthesised at 41°C maintained transcriptional activity even though genome replication failed. Reduced polymerase association with viral RNA was seen in vivo and in confirmation of this, in vitro binding assays showed that temperature increased the rate of dissociation of polymerase from both positive and negative sense promoters. However, the interaction of polymerase with the cRNA promoter was particularly heat labile, showing rapid dissociation even at 37°C. This suggested that vRNA synthesis fails at elevated temperatures because the polymerase does not bind the promoter. In support of this hypothesis, a mutant cRNA promoter with vRNA-like sequence elements supported vRNA synthesis at higher temperatures than the wild-type promoter.
The differential stability of negative and positive sense polymerase-promoter complexes explains why high temperature favours transcription over replication and has implications for the control of viral RNA synthesis at physiological temperatures. Furthermore, given the different body temperatures of birds and man, these finding suggest molecular hypotheses for how polymerase function may affect host range.
The genome of influenza A virus consists of eight single-stranded, negative-sense genomic RNA (vRNA) segments, associated with nucleoprotein (NP) and the viral polymerase complex (PB1, PB2 and PA) in the form of ribonucleoprotein complexes (RNP) . The viral RNA-dependent RNA polymerase is responsible for both transcription and replication of the viral genome, which take place in the cell nucleus [2, 3]. The first step in viral gene expression is the transcription of the incoming vRNPs into mRNA, through a primer-dependent process in which 5'-capped RNA fragments of 10–15 nt are cleaved from host-cell pre-mRNAs and used as primers . The resulting transcripts are polyadenylated at their 3' end when the polymerase, reiteratively incorporates A residues as a result of stalling at the polyuridine stretch [5–7] immediately adjacent to the 5' terminus of vRNA, to which the polymerase remains bound. These mRNA transcripts, being incomplete copies of the vRNA template, cannot serve as substrates for replication of new vRNA molecules. Viral genome replication is primer independent and generates full-length positive-sense cRNA transcripts, that are not polyadenylated [8–10]. This replicative intermediate subsequently serves as the template for synthesis of progeny vRNA.
The temporal pattern of RNA production is well established [11–15]. The replicative intermediate, cRNA, is first detected during the early stages of viral infection, reaches a maximum rate of synthesis prior to that of m- or vRNA and then declines. Maximal rates of mRNA synthesis also occur relatively early, before substantial amounts of vRNA are made. Amplification of vRNA continues even after m- and cRNA levels decline. Generally therefore, the early stages of viral infection can be defined by a prevalence of plus sense transcription, comprised mostly of mRNA with a minority of cRNA, while at later times negative sense replication in the form of vRNA synthesis is favoured. Various models have been proposed to explain the "switch" that regulates the transition from transcription to replication. De novo protein synthesis, and therefore a first round of viral transcription, is necessary for genome replication to occur [11, 13]. NP is undoubtedly required for both positive and negative sense genome replication [10, 16], but its precise role is not known [17–20]. Newly synthesized polymerase protects the termini of cRNA molecules from nuclease attack , which at least partly explains its requirement for the accumulation of cRNA. Some studies support the hypothesis that alternative forms of the polymerase catalyse transcription and replication, with a dimeric PB1-PA complex perhaps being the minimum requirement for genome replication [22, 23]. However, this is controversial with several other groups finding an essential role for PB2 in transcription and replication [24–26]. Host cell polypeptides may also be involved in the shift to genome replication [27–30], but this is uncertain.
Understanding the determinants of species tropism for influenza virus has never been more important than it is now, with the concern about the potential of avian H5N1 virus to adapt to human hosts. While tropism is a multifaceted and complex process, it has long been hypothesized that something as simple as the temperature at the site of replication could influence the host and tissue tropism of the virus [31–33]. Human-tropic influenza viruses are considered to replicate in the upper respiratory tract at 33–37°C, while avian influenza viruses replicate in the gut around 41°C . The polymerase is an important determinant of influenza virus host range and pathogenicity [34–39] that is likely to be influenced by temperature. Firstly it is a multifunctional enzyme, and secondly, the consequence of its interaction with the 5' and 3' termini of viral RNA is modulated by whether these regions are in a base-paired or single stranded conformation . We therefore examined the temperature dependency of polymerase function for mammalian adapted virus strains in cell culture and in vitro assay systems. We found that vRNA synthesis was markedly reduced at elevated temperatures, whereas mRNA synthesis was stimulated. We found no evidence to implicate heat shock proteins in this temperature effect, despite their known interaction with influenza A RNPs [30, 41]. The reduction of vRNA synthesis correlated with a markedly increased dissociation rate of the viral polymerase from cRNA at 41°C. Furthermore, we find that at 37°C the interaction of polymerase with cRNA was significantly less stable than with vRNA, a finding with implications for the regulation of viral RNA synthesis and for the adaptation of influenza viruses to host species with different body temperatures.
Effect of temperature on viral RNA synthesis
To test if the alteration in transcriptional balance at high temperature resulted from differential expression of the viral polypeptides, protein synthesis was analysed by 35S-methionine labelling. Time course analyses of infected cells showed similar patterns of viral protein synthesis at 37°C and 41°C (Fig. 1C, compare lanes 1–4 to lanes 6–9). Similar levels of polypeptides of the predicted size for HA, NP, M1, NS1 and NS2 were detected at both temperatures but were not present in mock-infected cells (Fig. 1C, lanes 5 and 10). Immunoprecipitation assays using antibodies against the three subunits of the viral polymerase also showed similar levels of PB1, PB2 and PA at both temperatures (Fig. 1D, compare lanes 1–3 to 4–6). Furthermore, the levels of co-precipitation of the three P proteins were similar at 41°C and 37°C, suggesting the polymerase complex is still formed at the higher temperature. No specific polypeptides were precipitated from mock-infected cell lysates by any of the three antibodies (lanes 7–12). The overall accumulation of PB1, M1 and NP were also found to be similar at either temperature by western blotting (data not shown). These results are consistent with the undiminished levels of viral mRNA observed at high temperature. Therefore, incubation of infected cells at 41°C does not substantially alter viral protein synthesis and the deficiency of any particular virus protein required for genome replication is an unlikely explanation for defective vRNA synthesis at high temperature.
The synthesis of NP and PB1 in transfected cells at the different incubation temperatures was analysed by western blotting. Temperature did not significantly alter the accumulation of either viral protein relative to a constitutively expressed cellular protein not known to be affected by temperature (Fig. 2C compare lanes 2–5 to 6–9). This suggests that similarly to authentic viral infection, alterations to the expression levels of viral proteins do not explain the temperature dependent change in the balance between viral transcription and replication.
Thus, the balance between transcription and replication of the influenza virus genome is affected by temperature in the settings of both infection and transfection, although a wider range of temperature affects the latter system.
Heat shock proteins as potential factors in the temperature-dependent inhibition of viral genome replication
Heat shock protein (hsp) synthesis and activity plays an important role in the cellular response to stress conditions, such as high temperature [42, 43]. Several reports have indicated an interaction between hsps and influenza virus RNP components. Hsp70 has been reported to interact with NP at 41°C and to consequently block vRNP nuclear export . Since NP is also intimately involved in viral RNA synthesis  it is possible that this cellular interaction might influence vRNA replication. Similarly, hsp90 has been suggested to bind two or more of the polymerase subunits at 37°C, with possible stimulatory or inhibitory effects on virus RNA synthesis [26, 30]. We therefore tested the hypothesis that hsp activity was responsible for the down-regulation of vRNA synthesis at 41°C.
Next, geldanamycin was used to interfere with hsp90 function. Hsp90 participates in two multichaperone complexes with opposing activities depending on the co-chaperone proteins attached to it. In one conformation the hsp90 complex binds to and stabilizes its client proteins, in the other, it promotes client protein ubiquitination and degradation by the proteasome. Geldanamycin binds to hsp90 and forces it to adopt the conformation that favours proteasome-targeting and prevents the stabilization function . 293T cells were inoculated with influenza virus and incubated at either 37°C or 41°C for 5 hours. Cells were either mock-treated or treated with 20 or 30 ng/ml of geldanamycin immediately after the virus adsorption period. Western blot analysis of the cell lysates showed decreasing levels of PB2 as the concentration of geldanamycin was increased at either temperature (Fig. 4C, lanes 3–5 and 8–10). This is consistent with a PB2-hsp90 interaction  that in the presence of geldanamycin results in the degradation of the client protein. Primer extension analysis for segment 2 was carried out on total cellular RNA extracted from these samples to test viral RNA synthesis during drug treatment. As previously observed for segment 2, levels of vRNA accumulation were lower, and those of mRNA higher, at 41°C compared to 37°C in non-treated cells (Fig. 4D, compare lane 3 to 8). However, when cells infected at 41°C were treated with either 20 or 30 ng/ml of geldanamycin the levels of vRNA remained low and in fact were further decreased by the drug (compare lanes 4 and 5 to 9 and 10).
Thus, at 41°C viral genome replication cannot be rescued by inhibiting hsp70 synthesis or hsp90 chaperone function, providing no support for the hypothesis that either of these cellular proteins is responsible for down-regulation of vRNA synthesis at high temperature, despite their known interactions with RNP components.
Analysis of the effect of temperature on RNP formation
Stability of polymerase-template interactions at elevated temperature
Here, we show that temperature dramatically affects the balance between transcription and replication of the influenza virus genome, with high temperature in particular favouring mRNA production over vRNA synthesis (Figs. 1 and 2). This effect was observed for both recombinant and authentic viral RNPs, for three strains of viral RNPs and in two different cell types, suggesting it is a general phenomenon for mammalian-adapted influenza A virus replication. The down regulation of vRNA synthesis at high temperature did not result from a deficiency of a viral polypeptide necessary for genome replication as no significant reduction was seen in the quantities of any of the viral proteins (Figs. 1, 2, 4 and data not shown). Although a recent report has suggested that NS1 is a necessary co-factor for vRNA synthesis , we found no defect in NS1 translation (Fig. 1C) and NS1 is clearly not required for replication in the recombinant system (Fig. 2). It was necessary to address the hypothesis that cellular heat shock proteins were responsible for the reduction in vRNA synthesis, as previous reports have indicated that hsp90 interacts with both PB2 and PB1-PA complexes at 37°C [26, 30] and that hsp70 binds NP at 37°C and 41°C . In vitro at 30°C, hsp90 stimulates ApG-primed transcription of an exogenous template added to virion-derived RNPs, while hsp70 has little effect . An interaction of hsp70 with NP has however been proposed to block M1-RNP interactions and consequently inhibit RNP nuclear export . However, the temperature dependent inhibition of genome replication showed no correlation with the amount of hsp70 and hsp90 present in cells. Heat shock prior to infection to induce hsp synthesis did not alter viral RNA synthesis at 37°C (Fig. 3). Furthermore, inhibition of hsp70 induction with quercetin did not rescue vRNA synthesis at 41°C (Fig. 4A). Similarly, geldanamycin-mediated inhibition of the chaperone function of hsp90 failed to rescue vRNA synthesis at 41°C (Fig. 4B). Hirayama et al. (2004) showed that in infected MDCK cells prostaglandin A1 (PGA) blocks NP nuclear export at 37°C and induces hsp70 expression without inhibiting viral gene expression. However, in 293-T cells we found that PGA inhibited all forms of viral RNA synthesis and viral protein expression (data not shown). Other studies have also noted inhibition of influenza virus gene expression by PGA and other prostaglandins and related compounds that induce hsp70 as well as a variety of other stress-related polypeptides [57, 58]. Overall therefore, although it is difficult to rule out categorically, we find no evidence in favour of the hypothesis that cellular hsp70 and/or 90 mediate the inhibition of viral genome replication at high temperature.
Two observations relating to the effects of hsps on virus replication are worthy of further comment. Firstly, while previous observations [41, 49] regarding the inhibition of NP nuclear export at 41°C were confirmed (Fig. 3), RNP formation was found to be abnormal, whereas the study of Sakaguchi et al (2003)  noted unaltered NP sedimentation behaviour on glycerol density gradients. The discrepancy between the two studies may result from the different gradient fractionation methods employed and the fact that Sakaguchi et al. looked solely at NP sedimentation and not RNA and polymerase protein sedimentation in addition to NP (reported here), which provides a more rigorous test of RNP formation (Fig. 5). Therefore, another contributing factor to the failure of NP nuclear export at 41°C is that RNP formation is much reduced. Secondly, the observation that moderate concentrations of geldanamycin inhibit PB2 accumulation at 37°C and 41°C, which is consistent with prior data indicating an interaction between this viral protein and hsp90 [26, 30] raises the possibility that geldanamycin may have antiviral activity against influenza A as well as a variety of other viruses [59–62].
The two-fold reduction in cRNA accumulation at 41°C might result from a reduced rate of synthesis, or from increased degradation of "naked" cRNPs, consistent with a recently suggested hypothesis for how cRNA synthesis is regulated . Increased degradation rates of RNPs may explain the apparently greater thermal sensitivity of recombinant RNPs (Figs. 2 and 8) because of the much longer timeframe of these assays (3 days compared to ≤ 8 h). The apparent paradox between increased levels of mRNA synthesis in the face of reduced vRNA levels may result from a higher rate of transcription of a reduced number of template molecules. This might reflect a Q10 effect of the higher temperature but may also result from loss of normal regulatory patterns (such as nuclear export of vRNA) during viral transcription. Consistent with the latter possibility, previous studies have noted substantial levels of mRNA transcription from a limited number of input vRNA templates when genome replication is blocked by cycloheximide [11, 12, 63].
At 37°C our finding that there is a negligible dissociation rate between polymerase and vRNA is consistent with the currently accepted mechanism for polyadenylation. In this hypothesis, the polymerase remains bound to the 5'-end of vRNA throughout mRNA transcription, thus forcing non-processive copying of a poly(U) stretch adjacent to the polymerase-binding site [6, 7, 54, 64, 65]. In light of recent research indicating that RNPs localise to specific regions within the nucleus [66, 67], a mechanism whereby vRNA molecules can be reiteratively copied without release of the polymerase seems likely to increase the efficiency of template usage. The significantly higher dissociation rate for polymerase-cRNA complexes at 37°C reflects a weaker interaction of the polymerase with the 5'-end of cRNA. This is consistent with the need to synthesise only full length copies from this template which presumably requires a template release step for each cycle of vRNA synthesis (Fig. 9). This is perhaps surprising given that large amounts of vRNA molecules are manufactured from a limited number of cRNAs whose synthesis apparently ceases early in infection [5, 68]. However, this quantitative difference in how the polymerase interacts with c- and vRNA promoters is consistent with recent research suggesting a qualitative difference in the mechanism used to initiate unprimed (replicative) transcription from the two strands .
Human influenza A virus, genome RNA synthesis is inhibited at high temperature, with transcription strongly favoured over replication. This temperature effect is due to the differential stability of negative and positive sense polymerase-promoter complexes, which is accentuated at high temperature (fig. 9). These findings have implications for the mechanisms that control normal viral RNA synthesis. Furthermore, as temperature is a notable physiological difference between avian and mammalian host systems, such considerations may have significance for the influence of avian virus-derived polymerase genes on host range and pathogenesis.
Cells, virus, plasmids, antibodies and other compounds
Human embryonic kidney 293T cells and Madin-Darby canine kidney (MDCK) cells were cultured in Dulbecco's modified Eagle's medium supplemented with L-glutamine, penicillin, streptomycin and 10% fetal calf serum (FCS). Influenza virus strain PR8 was propagated in 10-day-old embryonated eggs as described previously . Infections were carried out at a m.o.i. of 5 and generally harvested at 5 h.p.i.
Plasmids pcDNA-PB2, -PB1, -PA and -NP are described elsewhere [20, 44]. pPolI(-)NS.CAT.RT, containing an antisense CAT gene flanked by the non-coding sequences of influenza A/WSN/33 virus segment 8, under control of a human RNA polymerase I promoter (Pol-I) and upstream of a hepatitis δ ribozyme sequence, was generously provided by Ervin Fodor (University of Oxford). A similar positive-sense CAT reporter [pPol-I(+)NS.CAT] has also been previously described . Plasmids pPOLI-cCAT-RT wild type, 3'U-8'A mutant (C-G to U-A in 5'-end) and 3G-8C mutant (A-U to G-C in 3'-end) were kindly provided by G. Brownlee . Plasmids p5'3'v and p5'3'c contain the T7 RNA polymerase promoter immediately upstream of model vRNA and cRNA template sequences such that linearization with MboII and transcription with T7 RNA polymerase leads to the synthesis of run-off transcripts with the sequence: AGUAGAAACAAGGGUGUUUUUUCCCGGGAAUUCGGAUCCACACCCUGCUUUUGCUand AGCAAAAGCAGGGUGUGUGGAUCCGAAUUCCCGGGUAAAAAACACCCUUGUUUCUACU, where the underlined bold sequences correspond to the terminal regions of segment 8 (NS1) vRNA and cRNA respectively.
Nuclear extracts of HeLa cells co-infected with vaccinia recombinants expressing the PB1, PB2 and PA subunits of the PR8 polymerase (Vac3P) were prepared as described previously .
Rabbit polyclonal antisera to influenza A virus RNP and anti-PR8 PB2 (MBP-PB2-C), PB1 (PB1-F1) and PA (PA-F3) have been described previously [19, 71]. Mouse monoclonal anti-PB1 (aa 44–69) was kindly provided by Dr. Mark Krystal (Bristol-Myers Squibb). Antibodies to β-actin, Lamin associated polypeptide 2 (LAP-2) and clathrin heavy chain were purchased from Sigma-Aldrich, Biosciences Pharmingen and Santa Cruz, respectively. Antibody to hsc72/hsp70 was supplied by BD Bioscience. Anti-rabbit IgG antibody conjugated to fluorescein isothiocyanate was supplied by DAKO A/S and Alexa 594-conjugated anti-mouse IgG antibodies by Molecular Probes. HRP-conjugated anti-rabbit or mouse IgG was purchased from Amersham Biosciences.
Quercetin was purchased from Calbiochem and cycloheximide and geldanamycin from Sigma. Drugs were dissolved in dimethylsulfoxide (DMSO) and stored at -20°C, except quercetin, which was stored at 4°C.
Influenza virus gene-expression assay
To reconstitute RNPs, 1 × 106 293-T cells per 35 mm well in 1 ml complete medium were transfected in suspension with 0.25 μg each of pcDNA-PB1, -PB2, -PA and -NP and 50 ng of either pPolI(+) NS.CAT, pPolI(-)NS.CAT.RT, 3'-8' mutant or 3–8 mutant, using cationic liposomes (Lipofectin; Gibco-BRL). The total amount of DNA in each transfection mix was normalized by the addition of pcDNA3 vector. Transfected cells were incubated for three days before harvest .
Primer-extension analysis of viral RNA
Total cellular RNA was isolated using a commercial kit (SV Total RNA Isolation System; Promega) according to the manufacturer's instructions. After spectrophotometric quantification and normalization, RNA was reverse-transcribed using avian myeloblastosis virus reverse transcriptase (Promega) and the appropriate DNA oligonucleotides that had been 5' end-labelled with [γ-32P]ATP as previously described . Radiolabelled products were detected by autoradiography and quantified by densitometry using NIH Image software . The oligonucleotides used were 5'-GAACTGAGCAACCTTGCG-3' (for detection of vRNA-sense segment 1), 5'-GTACTTCTTGATTATGGC-3' (positive-sense segment 1), 5'-TCCAGTATGGTGGAGGC-3' (vRNA-sense segment 2), 5'-GTATCCTGTTCCTGTCCC-3' (positive-sense segment 2), 5'-CAAATAACATTTATGCAAGCC-3' (vRNA-sense segment 8) and 5'-TTAGGGATTTCTGATCTCGGC-3' (positive-sense segment 8). The oligonucleotides used to detect segments, 5, 7 and CAT have been previously described .
For Western blots, cell lysates were separated by SDS-PAGE and transferred to nitrocellulose. Blots were probed with primary followed by secondary antibodies conjugated to horse-radish peroxidase (DAKO) and developed by chemiluminescence (ECL reagent; Amersham Biosciences). Immunofluorescence assays were carried out as previously described [70, 44]. For metabolic labelling of proteins, 293T cells were washed twice with methionine-free medium for 5 min. and then incubated for 2 h with 60 nCi/μl of 35S-methionine For immunoprecipitation, 4 × 105 cells were labelled at 4 hpi as described above, then harvested in 200 μl IP buffer (50 mM Tris-HCl, pH7.6, 100 mM KCl, 5 mM MgCl2) containing 0.1% NP40 before being subjected to immunoprecipitation as previously described .
Velocity gradient centrifugation
8 × 106 293T cells were lysed with 1 ml of buffer containing 0.5% Triton X-100, 10 mM NaCl and 20 mM Tris-HCl (pH7.6), treated with 10 μg/ml Dnase I (Sigma), 5 mM MgCl2, 10 mM vanadyl ribonucleoside complex (New England Biolabs) for 15 min at 37°C and clarified at 3,000 rpm for 5 min at 4°C in a minicentrifuge. The supernatant was layered on top of a 12 ml continuous 5–20% (w/v) sucrose gradient in 20 mM Tris-Cl pH7.6, 50 mM NaCl, 0.1 mM EDTA and centrifuged at 100,000 gav for 13 h . Fractions were then collected and analysed for their protein and RNA content by western blot and primer extension respectively. For this, protein was concentrated by precipitation with methanol-chloroform  and RNA was isolated by phenol:chloroform extraction and ethanol precipitation.
Polymerase binding assays
The preparation of RNA transcripts labelled internally with [α-32P] GTP and the binding assay protocol have been described previously . 150 μl binding reactions containing 1.5 × 105 cpm of labelled probe (5'3'v or 5'3'c) were incubated with 30 μg of Vac 3P extract for 10 min at 22°C to allow the polymerase to bind to the RNA. Heparin was then added to a final concentration of 5 mg/ml, sufficient to inhibit all subsequent binding of the polymerase and displace non-specific RNA binding of other proteins in the extract. The binding reactions were then aliquoted into 12 separate tubes and incubated at either 31°C, 37°C or 41°C. At regular intervals, one tube from each temperature was removed and placed on ice until the completion of the time course. The samples were then analysed by non-denaturing electrophoresis and autoradiography as described previously .
We thank Professor George G. Brownlee for providing plasmids and Dr Debra Elton for advice and discussion. This work was supported by grants from the Wellcome Trust (no 073126) to PD and MRC grants (nos. G9901213 and G0300009 to LT and PD). MJA is supported by the Gulbenkian PhD program in Biomedicine and the Fundacao para a Ciencia e Tecnologia.
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