The Molecular Biology of Pneumovirus (BMP) group research focuses on Respiratory Syncytial virus (RSV) replication. Human RSV (HRSV) is the major cause of bronchiolitis and pneumonia in young children. It is one of the major infections for which there is no vaccine or antiviral treatment, Like the HRSV, bovine respiratory syncytial virus (BRSV) is also the chief viral respiratory pathogen of calves and is responsible for large economic losses in European dairy and beef farming. Although there is still no vaccine available for humans, some vaccines are commercialized for cattle but the efficiency is low. Development of new vaccine approaches and new broad spectrum antivirals is therefore an exciting scientific and economical alternative in both HRSV and BRSV. The main purpose of the BMP team is to study the functioning and the structure of the RNA polymerase complex, RSV-host interactions and virion assembly of Respiratory Syncytial virus (RSV), and to develop antiviral compounds based on these data. We also collaborate with immunologists (from VIM and from other labs) to develop new vaccine strategies using recombinant proteins.
RSV RNA replication and transcription
The group specializes in structural and functional analysis of some of the key RSV proteins required for replication. One of the main projects focuses on viral RNA replication and transcription, specifically the structural and functional analysis of Ribonucleoprotein (RNP) complex. Our team has built all the necessary tools to track the viral proteins within infected cells and on replicon system. We have set up a reverse genetics system allowing targeted modifications the viral genome and engineered fluorescent and luminescent RSV. We have also developed protocols to produce recombinant proteins for studying their structure and function in vitro, especially the different components of the RNP complex (M2-1, Phospho and Nucleo proteins).
Viral transcription and the transcription factor M2-1.
The RSV M2-1 protein is a transcription factor essential for efficient virus life cycle. In collaboration with the group of John Barr, Leeds University, U.K., we have first solved the atomic structure of this protein and showed that it binds preferentially to viral sequences present at the 3’ end of viral mRNAs (Tanner et al., 2014; PNAS). RSV RNA synthesis occurs in cytoplasmic inclusion bodies (IBs) where all the components of the RNA polymerase complex are concentrated. In collaboration with M.A. Rameix-Welti (UVSQ), we have demonstrated that viral RNA synthesis occurs in these IBs (Rincheval et al., 2017; Nat. Comm). By dissecting the ultrastructure of IBs, we found that RSV mRNAs form granules called IB associated granules (IBAGs), where M2-1 co-localizes. These results suggest a post-transcriptional role of M2-1. M2-1 is a phosphoprotein and cyclic phosphorylation/dephosphorylation of M2-1 is critical for viral transcription. We have also investigated the molecular mechanisms regulating M2-1 phosphorylation and found that RSV P protein captures the cellular phosphatase 1 (PP1) to dephosphorylate M2-1 in IBs, allowing M2-1 to bind to viral mRNAs (Richard et al., 2018; Plos Path.). Recently, we have also shown that expression of the RSV nucleoprotein N and phosphoprotein P of the polymerase complex is sufficient to induce the formation of pseudo-IBs. Moreover, we identified the domains of P required for IB formation and show that the oligomeric state of N is critical for their morphogenesis. We also show that pseudo-IBs can form in vitro when recombinant N and P proteins are mixed. Finally, using fluorescence recovery after photobleaching approaches, we reveal that in cells and in vitro IBs are liquid organelles (Galloux et al., 2021; mBio).
The RSV phosphoprotein
The RSV P protein plays a central role within the polymerase complex by interacting with L, N, and M2-1 to regulate the polymerase activity. We have mapped and characterized the L-binding region of RSV P protein. It is located in the C-terminal disordered region of P (Sourimant et al., 2015; J Virol). In the same time, we mapped the N binding region of P at the N-terminus of P (Galloux et al., 2015; J Virol). Finally, the PP1- and M2-1 binding sites of P were mapped to residues 82-87 and 93-110, respectively, by NMR (Richard et al., 2018; Plos Pathogens. In parallel, in collaboration with Christina Sizun, CNRS Gif-sur-Yvette, we have studied the structure of RSV P protein by NMR. We showed that RSV P has N- and C-terminal disordered regions, and that domains involved in the interactions with its viral partners present propensity to fold into secondary structure (Pereira et al., 2017; J Biol Chem).
The RSV Nucleoprotein.
The RSV RNA genome is enwrapped by the viral nucleoprotein N at all steps. This N-RNA complex is the template for the RNA-dependent RNA polymerase complex formed by P and L. Polymerization of N along the genomic and anti-genomic RNAs is concomitant to replication and requires the supply of neosynthetized N protein. This N protein is maintained monomeric and RNA-free through the interaction with the viral phosphoprotein P that plays the role of a chaperone, forming a soluble N -P complex. The interaction between P and N in this complex differs from the interaction between N-RNA and P. One main project was to characterize the N-P interactions in order to rationally design new antiviral approaches. First, we previously identified the P binding region on the N-RNA complex (Galloux et al., 2012; J Virol). By using in silico screenings, we selected some compounds that could bind to this pocket and interfere with the P-N interaction (Ouizougoun-Oubari et al., 2015; J Virol). Second, to investigate the structure of the N -P complex, we have engineered a mutant form of N which is monomeric, unable to bind RNA, still interacts with P, and could thus mimic the N monomer. We used this N mutant to show that the N-terminal region of P is directly involved in the chaperone activity of P required for the N -P complex formation (Galloux et al., 2015; J Virol). Our next objective is to determine the mechanism controlling the specificity of encapsidation of the genomic RNA by the N protein and to characterize the helical N-RNA protein complex.
The RSV Large polymerase L.
We have mapped the L binding domain on P using the baculovirus system (Sourimant et al., 2015; J Virol). The strucure of the L-P complex was then resolved by cryo-EM in collaboration with the group of Jason McLellan (Gilman et al., 2019; Cell). We also collaborate since several years with the big pharma Janssen-Cilag (J&J) which developed compounds inhibiting RSV replication, in order to identify the molecular target(s) of these compounds. Using an RSV minireplicon we have shown that some specific mutations on some RSV genes confer resistance to the compounds. We aim to resolve the structures of the L-compounds complexes.
RSV assembly and budding
Other project focuses on RSV assembly and budding, combining biochemical, functional and structural analysis of viral and cellular protein-protein interactions. The virus assembles and buds through the plasma membrane, forming elongated membrane filaments, but details of how this happens remain obscure. We have previously shown that M is biologically active as a dimer and that the switch from M dimers to higher oligomers triggers viral filament assembly and virus production (Forster et al., 2015; J Virol). It was shown previously that the Matrix (M), Phosphoprotein (P), and the Fusion (F) proteins of Respiratory syncytial virus (RSV) are sufficient to produce virus-like particles (VLPs) that resemble the RSV infection-induced virions. Our focus was the interaction between P and M during RSV assembly and budding. We showed that M interacts with P in the absence of other viral proteins in cells. By using recombinant proteins, we demonstrated a direct interaction between M and P. By using Nuclear Magnetic Resonance (NMR) we identified three novel M interaction sites on the N terminal domain of P, and the oligomerization domain (OD). We show that the OD, and likely the tetrameric structural organization of P, is required for virus-like filament formation and VLP release (Bajorek et al., 2021; J Virol).
We have previously used different protein-protein interaction screens to identify host factors binding to the RSV M, N, and NS1 protein. Our current goal is to characterize virus-cell interactions at the molecular level and to define molecular targets for the development of new antivirals. We are now focusing on host factors interacting with M and N during assembly. Other targets include nuclear host proteins interacting with NS1 and their possible link to IFN regulation during RSV infection.
HMPV RNA replication and transcription
As RSV, human metapneumovirus (HMPV) belongs to the pneumovirus family and is also an important respiratory pathogen in children. Helped by a collaboration with Janssen who financed the Ph.D. of Hortense Decool, we study the RNA polymerase complex of HMPV and characterize the molecular targets of potential antiviral compounds.