Influenza A virus preferentially snatches noncoding RNA caps

Abstract

Influenza A virus (IAV) lacks the enzyme for adding 5 ′ caps to its RNAs and snatches the 5 ′ ends of host capped RNAs to prime transcription. Neither the preference of the host RNA sequences snatched nor the effect of cap-snatching on host processes is completely defined. Previous studies of influenza cap-snatching used poly(A)-selected RNAs from infected cells or relied on annotated host genes to define the snatched host RNAs, and thus lack details on many noncoding host RNAs including snRNAs, snoRNAs, and promoter-associated capped small (cs)RNAs, which are made by "paused" Pol II during transcription initiation. In this study, we used a nonbiased technique, CapSeq, to identify host and viral-capped RNAs including nonpolyadenylated RNAs in the same samples, and investigated the substrate-product correlation between the host RNAs and the viral RNAs. We demonstrated that noncoding host RNAs, particularly U1 and U2, are the preferred cap-snatching source over mRNAs or pre-mRNAs. We also found that csRNAs are highly snatched by IAV. Because the functions of csRNAs remain mostly unknown, especially in somatic cells, our finding reveals that csRNAs at least play roles in the process of IAV infection. Our findings support a model where nascent RNAs including csRNAs are the preferred targets for cap-snatching by IAV and raise questions about how IAV might use snatching preferences to modulate host-mRNA splicing and transcription.

Comprehensive characterisation of molecular host-pathogen interactions in influenza A virus-infected human macrophages

“…Thus, at least two populations of snatched sequences exist: those that were 226 heavily snatched as they occur multiple times, and those that were seemingly randomly snatched 227 as they appear only once. Most (74%) of the leader sequences were between 10 and 14 228 nucleotides long (Figure 2 coinciding with levels of high transcription by the virus and are consistent with previous reports of 259 an 'AG' preference at the 5' end of the leader (Gu et al, 2015). 260…”

“…Possession of this sequence was therefore used to 194 identify viral transcripts. Similar to results seen elsewhere (Gu et al, 2015;195 Sikora et al, 2014), the A at the 5' end of the promoter was not always present and thus 196 sequences which contained the 11 nucleotide sequence 'GCAAAAGCAGG', referred to 197 subsequently as the IAV promoter, were brought forward for analysis. The IAV promoter is 198 present in all 8 viral mRNA segments and follows the host-derived leader sequence (Figure 2 A).…”

The Influenza Virus Polymerase Complex: An Update on Its Structure, Functions, and Significance for Antiviral Drug Design

“…The observation that the capped host RNAs is cleaved at a distance of 10–15 nucleotides from the 5ʹ‐cap can be explained by the 50 Å distance between the cap‐binding and endonuclease domains in the “open” FluA structure . Regarding the type of RNA substrate, the previous assumption that only host (pre‐)mRNAs are targeted, is contradicted by recent data that noncoding RNAs are the primary source of capped primers . The evidence for sequence preference is inconclusive, but recent deep sequencing studies indicate a preference for capped primers ending with a purine residue.…”

“…23 Regarding the type of RNA substrate, the previous assumption that only host (pre-)mRNAs are targeted, is contradicted by recent data that noncoding RNAs are the primary source of capped primers. [63][64][65] The evidence for sequence preference is inconclusive, 19,20,42,52,62,[66][67][68] but recent deep sequencing studies 63,69 indicate a preference for capped primers ending with a purine residue. The selection could be determined 20,[70][71][72] (i) at the level of RNA cleavage and/or (ii) transcription initiation when requiring base-complementarity between the 3ʹ end of the vRNA template and a given cellular RNA.…”

Role of MAPK/MNK1 signaling in virus replication

“…Most DNA viruses such as HSV-1, African swine fever virus (ASFV) (Castello et al, 2009), vaccinia virus (Walsh et al, 2008) as well as some RNA viruses such as chikungunya virus (CHIKV) (Walsh et al, 2013), SARS-CoV (Cencic et al, 2011), orthomyxoviruses (Aragon et al, 2000;Yanguez et al, 2012), rhabdoviruses (VSV, rabies virus) (Komarova et al, 2007), reoviruses (Chulu et al, 2010), hantavirus (Mir and Panganiban, 2008), and alphaviruses (Voss et al, 2014) contain a 5′ cap in their mRNA. Some of the viruses such as influenza virus steal the 5′ cap from the cellular mRNAs (Gu et al, 2015;Plotch et al, 1981) whereas several other viruses synthesize it by using hostencoded capping apparatus, for instance, vaccinia virus and reoviruses (Harwig et al, 2017). Viruses such as flaviviruses (Saeedi and Geiss, 2013) and nidoviruses synthesise the 5′ cap by their own capping apparatus (Harwig et al, 2017).…”