Nuclear export of Influenza RNA segments – NEPTUNE

Influenza A virus (IAV) is a highly infectious respiratory pathogen that continues to be a significant threat to global public health. Wild aquatic birds being the natural hosts for most IAV, they also infect multitudinous animal species in addition to humans. Due to his wildlife circulation and through recombination and/or genetic reassortment events, IAV is considered as one of the pandemic risk emerging pathogens. The fundamental understanding of IAV replication mechanism is thus key to the development of new therapeutic strategies. IAV genome is made of 8 RNA segments, called viral ribonucleoproteins (vRNPs). Each RNA segment is encapsidated by multiple copies of the viral nucleoprotein (NP) and bound to a single copy of the viral RNA-dependent RNA polymerase (RdRp), making the vRNP. Although vRNPs are central in the virus replication, a high-resolution structure is lacking and the NP-RNA mechanism of interaction is poorly understood. An important step in the virus life cycle is the nuclear export of progeny vRNPs. Several studies have demonstrated that both viral matrix 1 protein (M1) and nuclear export protein (NEP) are involved in the recruitment of the cellular exportin1 protein, leading to the nuclear export of the vRNPs, however, the precise molecular mechanism remains unclear.
In this context, the NEPTUNE project aims at providing an integrative and multiscale vision of the influenza replication complex. Using cutting-edge structural biology, biochemistry and virology, this multi-pronged proposal will elucidate the structural and molecular basis of (i) the viral RNA and NP assembly into a functional RNP and (ii) the vRNP nuclear export unexplored modus operandi. With the tools and protocols developed, other aspects of influenza replication will be addressed, such as the global cellular RNP trafficking or the host specificity.
NEPTUNE is coordinated by Allison Ballandras-Colas. Being an expert in cryoEM helical reconstructions, she has been recruited by the CNRS in 2021 in the “Institut de Biologie Structurale” (UMR5075, Grenoble) to work on RNA virus replication, and on influenza in particular. She will benefit from the expertise of other members of the institute, in particular regarding other structural biology technics, and the unique environment for state-of-the-art integrated structural biology in Grenoble, such as the ISBG (UMS 3518) or the Partnership for Structural Biology. Structural data will be validated in vivo through a collaboration established with Nadia Naffakh (UMR3569, Institut Pasteur) who has a long-standing interest in IAV biology.
By providing the first high-resolution model showing how RNA is organized within the RNP, NEPTUNE represents the ultimate source to understand how RNPs could interact altogether during influenza packaging and/or reassortment events that could end to a potential new pandemic virus. Furthermore, IAV RNP being an ideal plural-target for drug design to generate novel antiviral and/or host-pathogen candidates, the structural data obtained within the context of the NEPTUNE can provide original strategies to intensify the fight against this major pathogen. We expect that the technical benefits of the project can also be applied to other segmented viral models and thus potentially promote research against other pathogens.