Influenza virus mRNAs encode determinants for nuclear export via the cellular TREX-2 complex

Abstract

Nuclear export of influenza A virus (IAV) mRNAs occurs through the nuclear pore complex (NPC). Using the Auxin-Induced Degron (AID) system to rapidly degrade proteins, we show that among the nucleoporins localized at the nucleoplasmic side of the NPC, TPR is the key nucleoporin required for nuclear export of influenza virus mRNAs. TPR recruits the TRanscription and EXport complex (TREX)−2 to the NPC for exporting a subset of cellular mRNAs. By degrading components of the TREX-2 complex (GANP, Germinal-center Associated Nuclear Protein; PCID2, PCI domain containing 2), we show that influenza mRNAs require the TREX-2 complex for nuclear export and replication. Furthermore, we found that cellular mRNAs whose export is dependent on GANP have a small number of exons, a high mean exon length, long 3’ UTR, and low GC content. Some of these features are shared by influenza virus mRNAs. Additionally, we identified a 45 nucleotide RNA signal from influenza virus HA mRNA that is sufficient to mediate GANP-dependent mRNA export. Thus, we report a role for the TREX-2 complex in nuclear export of influenza mRNAs and identified RNA determinants associated with the TREX-2-dependent mRNA export.

Identifying cellular RNA-binding proteins during infection uncovers a role for MKRN2 in influenza mRNA trafficking

“…IAV mRNA synthesis is further complicated by the fact that, minimally, 8 out of the 10 predominant IAV mRNAs are not spliced. 20 Splicing in eukaryotic cells generally leads to the direct recruitment of nuclear export factors such as NXF1 followed by the rapid trafficking of spliced mRNA to the cytoplasm. 21 However, this is not the case for the majority of IAV transcripts, and successful replication necessitates other means to effectively export IAV mRNAs.…”

“…22 A recent study has implicated a role for the TREX-2 complex in the nuclear-cytoplasmic trafficking of IAV mRNAs. 20 The authors found that the nucleoporin, TPR, is important for this process via its recruitment of TREX-2 to the nuclear pore complex (NPC). For a subset of cellular mRNAs, and it seems IAV mRNAs, that are exported via this process, NXF1 is recruited by GANP, a component of TREX-2, which then leads to mRNA trafficking through the NPC.…”

“…For a subset of cellular mRNAs, and it seems IAV mRNAs, that are exported via this process, NXF1 is recruited by GANP, a component of TREX-2, which then leads to mRNA trafficking through the NPC. 20 GLE1 is then involved in release of NXF1 which is then recycled back into the nucleus. An earlier study investigated the dependence of various known mRNA export factors for IAV mRNA export.…”

“…12 In particular, this method could provide a more thorough understanding into how intronless IAV mRNAs escape the nucleus after transcription. Though this is still an open question, a recent study by Bhat et al (2023) has shed some light on this process of nuclear-cytoplasmic trafficking. The authors reported that the TREX-2 complex is recruited to viral mRNAs, then through an association with NXF1, the viral mRNAs are efficiently exported via the nuclear pore complex (NPC) to the cytoplasm.…”

Export of discarded splicing intermediates requires mRNA export factors and the nuclear basket

“…The N-termini of these proteins are anchored to the nuclear pore, and their C-termini extend roughly 300 nm into the nuclear interior (Bangs et al, 1998; Kim et al, 2018). In addition to the purported roles in retaining immature RNAs in the nucleus, Mlp1p and TPR have been implicated in mRNA export in S. pombe , Arabidopsis , and mammalian cells as perturbations of these proteins result in the accumulation of poly(A)+ RNA in the nucleus and/or defects in export of specific mRNAs to the cytoplasm (Aksenova et al, 2020; Bae et al, 2009; Bhat et al, 2023; Lee et al, 2020; Li et al, 2021; Shibata et al, 2002; Umlauf et al, 2013; Xu et al, 2007; Zuckerman et al, 2020). Indeed, rapid depletion of TPR and NXF1 results in similar mRNA export defects (Aksenova et al, 2020; Zuckerman et al, 2020), supporting an mRNA export role for TPR, which microscopy implies functions in mRNA docking to the NPC (Aksenova et al, 2020; Lee et al, 2020; Li et al, 2021).…”