Structural and functional organization of Ebola virus induced cytoplasmic inclusion bodies

• Applicant: Dr. Melina Vallbracht
• Subject Area: Virology ; Structural Biology
• Term: from 2021 to 2023
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 469065579

• Final Report Year: 2024

Final Report Abstract

Viral RNA synthesis and genome encapsidation of the highly pathogenic Ebola virus (EBOV) and many other negative-sense RNA viruses take place in virus-induced cytoplasmic membrane-less organelles termed inclusion bodies (IBs). However, the structural and functional organization of EBOV IBs and their interactions with the cellular environment remain largely unknown. In the course of the project, we applied state-of-the-art cryo-correlative light and electron microscopy and in situ cryo-electron tomography (cryo-ET) and complementary techniques to elucidate structural changes of EBOV IBs during the course of an infection. Within the funding period of the Walter Benjamin Program, we were able to report several achievements. We not only unraveled the structure of assembling EBOV nucleocapsids (NCs) within the IBs at different stages of infection but also showed that their assembly has a direct impact on the physical properties of the IBs. We show that EBOV NCs transition from loosely packed helical assemblies in early IBs to condensed cylinders that arrange into highly organized parallel bundles later in infection. This VP24-driven condensation process drives a concomitant reduction in IB fluidity which leads to dispersion of the condensate into the cytoplasm. The resulting loss of IB integrity serves as a switch that allows the condensate material to interact with cellular components such as the actin cytoskeleton promoting viral egress. In summary, our findings significantly expand our understanding of the structural and functional organization of EBOV IBs and highlight a complex interplay between NC assembly, liquid organelle coarsening, and the interaction between the viral factories and the host cytoskeleton.

Publications

• EMBO | EMBL Symposium: Cellular mechanisms driven by phase separation, EMBL- Heidelberg, Germany (05/2022) “Investigating the molecular architecture of Ebola virus induced cytoplasmic inclusion bodies by in cellulo cryo-CLEM
  Vallbracht M., Bodemer B.S., Hoenen T. & Chlanda P.
  
• NSV 2022, Braga, Portugal (06/2022) “Structural insight into the Ebola virus nucleocapsid assembly cascade by in-cell cryocorrelative light and electron microscopy”
  Vallbracht M., Bodmer B.S., Winter S., Hoenen T. & Chlanda P.
  
• 32nd Annual Meeting of the Society of Virology, Ulm, Germany (3/2023) “Structural insight into the Ebola virus nucleocapsid assembly cascade by in-cell cryoelectron tomography”
  Vallbracht M., Bodmer B.S., Fischer K., Winter S., Hoenen T. & Chlanda P.
  
• Ebola virus inclusion bodies are liquid organelles whose formation is facilitated by nucleoprotein oligomerization. Emerging Microbes & Infections, 12(2).
  Bodmer, Bianca S.; Vallbracht, Melina; Ushakov, Dmitry S.; Wendt, Lisa; Chlanda, Petr & Hoenen, Thomas
  
• EMBO Workshop: In situ structural biology: from cryo-EM to multi-scale modelling, Heidelberg, Germany (02/2023) “Structural insight into the Ebola virus nucleocapsid assembly cascade by in-cell cryo- CLEM”
  Vallbracht M., Bodmer B.S., Winter S., Hoenen T. & Chlanda P.
  
• In vivo characterization of the novel ebolavirus Bombali virus suggests a low pathogenic potential for humans. Emerging Microbes & Infections, 12(1).
  Bodmer, B. S.; Breithaupt, A.; Heung, M.; Brunetti, J. E.; Henkel, C.; Müller-Guhl, J.; Rodríguez, E.; Wendt, L.; Winter, S. L.; Vallbracht, M.; Müller, A.; Römer, S.; Chlanda, P.; Muñoz-Fontela, C.; Hoenen, T. & Escudero-Pérez, B.
  
• Nucleocapsid condensation drives Ebola viral factory maturation and dispersion. openRxiv.
  Vallbracht, Melina; Bodmer, Bianca S.; Fischer, Konstantin; Makroczyova, Jana; Winter, Sophie L.; Wendt, Lisa; Wachsmuth-Melm, Moritz; Hoenen, Thomas & Chlanda, Petr
  
• The Ebola virus VP40 matrix layer undergoes endosomal disassembly essential for membrane fusion. The EMBO Journal, 42(11).
  Winter, Sophie L.; Golani, Gonen; Lolicato, Fabio; Vallbracht, Melina; Thiyagarajah, Keerthihan; Ahmed, Samy Sid; Lüchtenborg, Christian; Fackler, Oliver T.; Brügger, Britta; Hoenen, Thomas; Nickel, Walter; Schwarz, Ulrich S. & Chlanda, Petr