PT  - JOURNAL ARTICLE
AU  - Aartjan J.W. te Velthuis
AU  - Judith Oymans
TI  - Initiation, elongation and realignment during influenza virus mRNA synthesis
AID  - 10.1101/197210
DP  - 2017 Jan 01
TA  - bioRxiv
PG  - 197210
4099  - http://biorxiv.org/content/early/2017/10/02/197210.short
4100  - http://biorxiv.org/content/early/2017/10/02/197210.full
AB  - The RNA-dependent RNA polymerase (RdRp) of the influenza A virus replicates and transcribes the viral genome segments in the nucleus of the host cell. To transcribe these viral genome segments, the RdRp ‘snatches’ capped RNA oligonucleotides from nascent host cell mRNAs and aligns these primers to the ultimate or penultimate nucleotide of the segments for the initiation of viral mRNA synthesis. It has been proposed that this initiation process is not processive and that the RdRp uses a prime-realign mechanism during transcription. Here we provide in vitro evidence for the existence of this transcriptional prime-realign mechanism, but show that it only functions efficiently for primers that are not stably base paired with the template. In addition, we demonstrate that transcriptional elongation is dependent on the priming loop of the PB1 subunit of the RdRp. We propose that the prime-realign mechanism may be used to rescue abortive transcription initiation events or cope with sequence variation among primers. Overall, these observations advance our mechanistic understanding of how the influenza A virus initiates transcription correctly and efficiently.Importance The influenza A virus causes severe disease in both humans and birds and is considered a major global health threat. The virus replicates and transcribes its genome using an enzyme called the RNA polymerases. To ensure that the genome is amplified faithfully and abundant viral mRNAs are made for viral protein synthesis the RNA polymerase must transcribe the viral genome efficiently. In this report, we characterise the role of a structure inside the polymerase that helps control the enzyme how viral mRNA molecules are synthesised.