Positive-sense RNA viruses reveal the complexity and dynamics of the cellular and viral epitranscriptomes during infection

Abstract

More than 140 post-transcriptional modifications (PTMs) are known to decorate cellular RNAs, but their incidence, identity and significance in viral RNA are still largely unknown. We have developed an agnostic analytical approach to comprehensively survey PTMs on viral and cellular RNAs. Specifically, we used mass spectrometry to analyze PTMs on total RNA isolated from cells infected with Zika virus, Dengue virus, hepatitis C virus (HCV), poliovirus and human immunodeficiency virus type 1. All five RNA viruses significantly altered global PTM landscapes. Examination of PTM profiles of individual viral genomes isolated by affinity capture revealed a plethora of PTMs on viral RNAs, which far exceeds the handful of well-characterized modifications. Direct comparison of viral epitranscriptomes identified common and virus-specific PTMs. In particular, specific dimethylcytosine modifications were only present in total RNA from virus-infected cells, and in intracellular HCV RNA, and viral RNA from Zika and HCV virions. Moreover, dimethylcytosine abundance during viral infection was modulated by the cellular DEAD-box RNA helicase DDX6. By opening the Pandora’s box on viral PTMs, this report presents numerous questions and hypotheses on PTM function and strongly supports PTMs as a new tier of regulation by which RNA viruses subvert the host and evade cellular surveillance systems.

The methyltransferase domain of the Sudan ebolavirus L protein specifically targets internal adenosines of RNA substrates, in addition to the cap structure

“…However, it has recently been shown that flavivirus MTases (Dengue virus and Zika virus) additionally carry out internal A-2'O methylations (29,34). These activities might be related to the epitranscriptomic RNA modifications recently reported in the genome of flaviviruses (52). Here, we report for the first time that internal A-2'O MTase activity also exists in viruses belonging to the Mononegavirales order (i.e.…”

Acetylation of cytidine residues boosts HIV-1 gene expression by increasing viral RNA stability

“…Finally N m has been reported to increase HIV-1 replication indirectly by preventing the activation of the host innate immune factor MDA5 by viral transcripts 15 . Here, we extend this previous work by looking at a novel epitranscriptomic modification, ac4C, that has been proposed to boost cellular mRNA translation and stability 12 and that has also been detected on purified HIV-1 genomic RNA 16 . We have mapped the ac4C residues present on HIV-1 RNAs to ~11 distinct sites and show that these are, as expected, deposited by the host acetyltransferase NAT10, as inhibition of NAT10 expression results in a loss of ac4C from viral RNAs (Fig.1).…”

“…While m 6 A, m 5 C and N m have therefore all been shown to increase HIV-1 gene expression, several other epitranscriptomic mRNA modifications remain unexamined. Of particular interest is the novel mRNA modification ac4C, which was recently reported to enhance cellular mRNA translation and stability 12 and which has previously been reported to represent ~0.5% of all nucleotides (~2% of “C” residues) on the HIV-1 genomic RNA (gRNA), which would equate to ~8 ac4C residues per gRNA 16 . We therefore hypothesized that addition of ac4C residues to HIV-1 transcripts might also serve to boost HIV-1 gene expression and replication.…”

Zika Virus Subverts Stress Granules to Promote and Restrict Viral Gene Expression

“…Such changes in PABP would be expected to negatively affect translation of cellular mRNAs and promote ZIKV gene expression. Moreover, Ataxin-2 interacts with the cellular RNA DEAD-box helicase DDX6 (54), which we have previously shown to be required for ZIKV gene expression (55). Therefore, the impact on ZIKV RNA and production of infectious particles ( Figure 3B and 3C) following RNAi depletion of Ataxin-2 might also be the result of changes to DDX6.…”