Heterologous influenza vRNA segments with identical non-coding sequences stimulate viral RNA replication in trans
© Ng et al; licensee BioMed Central Ltd. 2008
Received: 10 October 2007
Accepted: 11 January 2008
Published: 11 January 2008
The initiation of transcription and replication of influenza A virus requires the 5' and 3' ends of vRNA. Here, the role of segment-specific non-coding sequences of influenza A virus on viral RNA synthesis was studied. Recombinant viruses, with the nonstructural protein (NS) segment-specific non-coding sequences replaced by the corresponding sequences of the neuraminidase (NA) segment, were characterized. The NS and NA vRNA levels in cells infected with these mutants were much higher than those of the wild type, whereas the NS and NA mRNA levels of the mutants were comparable to the wild-type levels. By contrast, the PB2 vRNA and mRNA levels of all the tested viruses were similar, indicating that vRNA with heterologous segment-specific non-coding sequences was not affected by the mutations. The observations suggested that, with the cooperation between the homologous 5' and 3'segment-specific sequences, the introduced mutations could specifically enhance the replication of NA and NS vRNA.
The genome of influenza A virus contains 8 RNA segments of negative polarity . Each virion RNA (vRNA) can be used as a template for transcription and replication to generate viral mRNA and complementary RNA (cRNA), respectively. cRNA is a faithful complementary copy of vRNA and is used as a template for vRNA synthesis. By contrast, the transcription of the viral mRNA is terminated at a track of uridines (U) which is about 17 nucleotides away from the 5' end of the vRNA template [2, 3] and the polymerase then starts to polyadenlyate the mRNA by reiteratively copying of the U-track [4, 5]. It is generally believed that there is a control mechanism to regulate the polymerase's transcriptase and replicase activities . However, recent studies have suggested an alternative hypothesis that such switching mechanism might not exist [7–10].
Sequence analyses of all the vRNA segments revealed that the first 12 and 13 nucleotides at their 3' and 5' ends are highly conserved . Extensive studies on these sequences indicated that these regions are the promoter for transcription and replication. These sequences were shown to be involved in the viral polymerase binding [12–14], cap-snatching [14, 15], and transcription initiation [16, 17]. The 5' and 3' ends of each vRNA are partially inverted complementary and can form a corkscrew structure that is known to be critical for the above biological processes . Within these conserved sequences, there is a single natural variation (U or C) at the 4th residue of the 3' end . Of all the vRNA segments, the polymerase segments (PB2, PB1 and PA) invariably carry a C residue at this position (C4), whereas most of the other segments contain a U residue at this position (U4). Mutagenic studies of this polymorphic site suggested that this nucleotide variation might modulate viral transcription and replication [18, 19]. Adjacent to the universally conserved regions, each vRNA segment contains additional non-coding sequences at its 5' and 3' regions. The lengths and sequences of these non-coding sequences are segment specific. Growing evidences have supported the hypothesis that these sequences are parts of the viral RNA packaging signals [20–24]. In addition, disrupting the NA segment-specific sequences were shown to have effects on viral RNA synthesis [25–27], indicating these segment specific sequences might modulate viral RNA synthesis.
One of the possible mechanisms account for the elevation of NS and NA vRNA levels is that the 5' and 3' segment-specific regions would facilitate the initiation of vRNA replication. This stimulating effect, however, might require the presence of the 5' and 3' segment-specific regions from homologous segments. As the NA and NS vRNA segments in the NSNA and NSNA-U mutants had the identical non-coding sequences, the availability of compatible 5' ends for initiating NS and NA vRNA replications would be increased. This hypothesis is supported by two of our observations. First, our data demonstrated that the mutations had no effect on vRNA which has heterologous segment-specific sequences (i.e. PB2). In addition, our data showed that the transcription of the NA and NS segments were not up-regulated. These agreed with previous findings that the viral polymerase has to bind to the 5' and 3' ends of the same vRNA template for mRNA synthesis [12, 29]. Thus, the increases of compatible ends' populations would not expected to have stimulating effects on the NS and NA mRNA expressions. Interestingly, the NS mRNA levels from the NSNA and NSNA-U mutants in this study seemed to be less than that of the corresponding controls (Figs. 2B and 3B, right panels). It is possible that, due to the increase of the number of these compatible ends in infected cells, the polymerase might have less chance to bind to the ends of the same vRNA template for transcription initiation.
In the early phase of viral infections, vRNP predominantly synthesizes mRNA for viral protein synthesis . This is followed by an active phase of viral RNA replication. It was previously proposed that the nascent NP expressed in infected cells might stimulate viral RNA replication [31, 32]. Recent evidences have provided an alternative hypothesis to explain this observation. Rather than stimulating the viral RNA replication, free NP and viral polymerase are proposed to protect nascent cRNA from degradation by binding to these newly synthesized cRNA transcripts [7, 9, 33]. The results from our current study might also help to explain the dramatic increase of cRNA levels in the late phase of viral infection. In the early phase of infection, the amount of vRNA is low and the viral polymerase is more likely to bind to the ends of the same vRNA template for transcription (i.e. activate in cis). Messenger RNA generated from this cis-acting transcription mode would be transported to cytosol for protein expression. Due to the lack of newly synthesized NP and viral polymerase, nascent cRNA generated from this cis-acting mode might be rapidly degraded at the early time point [7, 9, 33]. By contrast, during the mid- to late phase of infection, the accumulations of cRNP and vRNP make the viral polymerase complex has less chance to bind to the ends from the same vRNA or cRNA template. At this stage, the viral RNA polymerase is prone to utilize the vRNA/cRNA ends derived from different templates from transcription initiation (i.e. trans-activation mode). As the polyadenylation of viral mRNA requires the viral polymerase bind to the same viral template [12, 29], transcription initiated by the trans-activation mode would favor viral RNA replication and further increase the vRNA and cRNA levels. In our study, the mutated NS segment could specifically enhance the NA vRNA and cRNA levels, suggesting the trans-activation mode might require the 5' and 3' vRNA ends derived from homologous RNA segments.
In conclusion, our result demonstrated that the segment specific regions have roles in controlling viral transcription and replication. Viral RNA with compatible segment-specific sequences might facilitate viral replication in trans. Given the fact that different viral RNA segments might have subtle sequence requirements for viral RNA synthesis , further studies on the segment-specific non-coding regions in other viral segments are needed.
This project is supported by National Institutes of Health (NIAID contract HHSN266200700005C), Research Grant Council of Hong Kong (HKU 7356/03M to LLMP) and Area of Excellence Scheme of the University Grants Committee (Grant AoE/M-12/06). We thank RG Webster (St. Jude Children's Research Hospital, Memphis, USA) for plasmids.
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